Plasmodium falciparum antigens and methods of use

ABSTRACT

The subject invention provides novel  Plasmodium falciparum  antigens and novel polynucleotides encoding these antigens. Also provided by the subject invention are methods of using these antigens and polynucleotides.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.10/537,642, filed Dec. 27, 2005, which is the national stage of PCTApplication No. PCT/US2003/038966, filed Dec. 8, 2003, which claims thebenefit of U.S. Provisional Application Ser. No. 60/431,494, filed Dec.6, 2002, the disclosure of each of which is incorporated herein byreference in its entirety, including all figures, tables, nucleic acidsequences, amino acid sequences, and drawings.

The Sequence Listing for this application is labeled “Seq-List.txt”which was created on Feb. 24, 2004 and is 566 KB. The entire contents ofthe sequence listing is incorporated herein by reference in itsentirety.

This invention was made with government support under Grant No. 1R43AI49051-01 awarded by NIAID. The government has certain rights in theinvention.

BACKGROUND OF INVENTION

The recent explosion in genomic sequencing has deposited a wealth ofinformation in the hands of researchers. However, there is not yet ameans to efficiently analyze such data to identify which antigens amongmany thousands are appropriate targets for vaccine development.

More than 5000 proteins are expressed during the life cycle of thePlasmodium spp. parasite. Subunit vaccines currently in development arebased on a single or few antigens and may therefore, elicit too narrow abreadth of response, providing neither optimal protection nor protectionon genetically diverse backgrounds. By contrast, to duplicate theprotection induced by whole organism vaccination (Good, M. F. & Doolan,D. L. Immune effector mechanisms in malaria. Curr. Opin. Immunol. 11,412-419 (1999)), a malaria vaccine targeting an unprecedented number ofparasite-derived proteins through inclusion of their minimal CD8⁺ andCD4⁺ T cell epitopes in a multiepitope construct appears to be required.However, the antigens mediating whole organism induced protection arelargely unknown.

Because of various factors, principally related to antigen abundance andimmunodominance, not all possible antigens are recognized by naturalimmunity (Yewdell J W, Bennink J R. Immunodominance in majorhistocompatibility complex class I-restricted T lymphocyte responses.Annu. Rev. Immunol. 17, 51-88. (1999)). Various approaches have beenproposed for antigen identification, including expression cloning(Kawakami, Y. & Rosenberg, S. A. Immunobiology of human melanomaantigens MART-1 and gp100 and their use for immuno-gene therapy. Int.Rev. Immunol. 14, 173-192 (1997)), elution and mass spectrometrysequencing of naturally processed MHC-bound peptides (Rotzschke, O. etal. Isolation and analysis of naturally processed viral peptides asrecognized by cytotoxic T cells. Nature 348, 252-254 (1990); van Bleek,G. M. & Nathenson, S. G. Isolation of an endogenously processedimmunodominant viral peptide from the class I H-2 Kb molecule. Nature348, 213-216 (1990); Hunt, D. F. et al. Peptides presented to the immunesystem by the murine class II major histocompatibility complex molecule1-Ad. Science 256, 1817-1820 (1992); Cox, A. L. et al. Identification ofa peptide recognized by five melanoma-specific human cytotoxic T celllines. Science 264, 716-719 (1994)), in vitro testing of pools ofoverlapping peptides (Kern, F. et al. Cytomegalovirus (CMV)Phosphoprotein 65 Makes a Large Contribution to Shaping the T CellRepertoire in CMV-Exposed Individuals. J. Infect. Dis. 185, 1709-1716(2002)), and reverse immunogenetics (Davenport, M. P. & Hill, A. V.Reverse immunogenetics: from HLA-disease associations to vaccinecandidates. Mol. Med. Today 2, 38-45 (1996); Aidoo, M. et al.Identification of conserved antigenic components for a cytotoxic Tlymphocyte-inducing vaccine against malaria. Lancet 345, 1003-1007(1995)). However, these methods suffer from potential problems such asthe repeated identification of the same (frequent/dominant) epitope,biases at the level of expansion of T cell populations, and use ofclonal/oligoclonal T cells. They also tend to underestimate thecomplexity of responses, and are not able to analyze a large number ofpotential targets in the context of multiple HLA types. Finally, none ofthese approaches easily lends itself towards the daunting task ofefficiently analyzing large amounts of genomic sequence data.

BRIEF SUMMARY

The subject invention also provides novel Plasmodium falciparum antigensthat are useful in therapeutic and diagnostic applications. In variousaspects, the subject invention provides embodiments such as:

-   -   A) isolated and/or purified polynucleotide sequences comprising:        -   a) a polynucleotide sequence encoding a polypeptide sequence            selected from the group consisting of SEQ ID NO: 1, 2, 3, 4,            5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,            21, 22, 23, 24, 25, 26, and 27;        -   b) a complementary polynucleotide sequence to a            polynucleotide sequence encoding a polypeptide sequence            selected from the group consisting of SEQ ID NO: 1, 2, 3, 4,            5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,            21, 22, 23, 24, 25, 26, and 27;        -   c) a polynucleotide sequence having at least about 20% to            99.99% identity to a polynucleotide sequence of A(a) or            A(b);        -   d) a fragment of a polynucleotide sequence according to A(a)            or A(b);        -   e) a polynucleotide sequence encoding a polypeptide as set            forth in Table 2, 3, 4, 5, or 6, or a polynucleotide            sequence encoding a polypeptide selected from the group            consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,            12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,            and 27;        -   f) a polynucleotide sequence encoding a variant of a            polypeptide (e.g., a variant polypeptide) selected from the            group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9,            10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,            25, 26, and 27;

g) a polynucleotide sequence encoding a polypeptide fragment of apolypeptide selected from the group consisting of SEQ ID NO: 1, 2, 3, 4,5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,24, 25, 26, and 27, wherein the fragment has substantially the sameserologic reactivity as the native polypeptide and/or substantially thesame T-cell reactivity as the native polypeptide or fragment;

-   -   -   h) a polynucleotide sequence encoding a fragment of a            variant polypeptide of a polypeptide selected from the group            consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,            12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,            and 27, wherein the fragment of the variant polypeptide has            substantially the same serologic activity as the native            polypeptide or substantially the same T-cell reactivity as            the native polypeptide or fragment; or        -   i) a polynucleotide sequence encoding a multi-epitope            construct;

    -   B) primers or detection probes (e.g., fragments of the disclosed        polynucleotide sequences) for hybridization with a target        sequence or the amplicon generated from the target sequence        comprising a sequence of at least 8, 9, 10, 11, 12, 13, 14, 15,        16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35,        40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100        consecutive nucleotides of the polynucleotide sequences set        forth herein. Labeled probes or primers are labeled with a        radioactive compound or with another type of label as set forth        in embodiment C, below;

    -   C) isolated polynucleotides according to embodiments A or B        further comprising a label; labels can include, and are not        limited to 1) radioactive labels, 2) enzyme labels, 3)        chemiluminescent labels, 4) fluorescent labels, 5) magnetic        labels, or other suitable labels. Exemplary labels include, and        are not limited to, ³²P, ³⁵S, ³H, ¹²⁵I, biotin,        acetylaminofluorene, digoxigenin, 5-bromo-deoxyuridine, or        fluorescein;

    -   D) methods of detecting P. falciparum in biological samples        comprising contacting a biological sample with isolated        polynucleotides of embodiments A, B, or C. In this        embodiment, P. falciparum cells, or cells comprising (infected)        by P. falciparum are recovered, lysed, and DNA and/or RNA are        extracted from the lysed cells. The extracted DNA or RNA is then        tested using polynucleotides and/or probes set forth herein for        the presence of P. falciparum. Typical assay formats utilizing        nucleic acid hybridization includes, and are not limited to, 1)        nuclear run-on assay, 2) slot blot assay, 3) northern blot assay        (Alwine, et al. Proc. Natl. Acad. Sci. 74:5350), 4) magnetic        particle separation, 5) nucleic Acid or DNA chips, 6) reverse        Northern blot assay, 7) dot blot assay, 8) in situ        hybridization, 9) RNase protection assay (Melton, et al. Nuc.        Acids Res. 12:7035 and as described in the 1998 catalog of        Ambion, Inc., Austin, Tex.), 10) ligase chain reaction, 11)        polymerase chain reaction (PCR), 12) reverse transcriptase        (RT)-PCR (Berchtold, et al. Nuc. Acids. Res. 17:453), 13)        differential display RT-PCR (DDRT-PCR) or other suitable        combinations of techniques and assays;

    -   E) analytical systems, such as DNA chips comprising        polynucleotide sequences according to embodiments A, B, or C;

    -   F) modified polynucleotide sequences comprising polynucleotide        sequences according to embodiments A or B;

    -   G) a polynucleotide sequence according to embodiments A, B, or        F, further comprising regulatory sequences, such as promoters,        enhancer elements, or termination sequences, that are operably        linked to the polynucleotide sequences of embodiments A or B;

    -   H) a vector comprising a promoter operably linked to a nucleic        acid sequence of the subject invention (e.g., as set forth in        embodiments A, B, or F), optionally, one or more origins of        replication, and, optionally, one or more selectable markers        (e.g., an antibiotic resistance gene);

    -   I) host cells transformed by a vector according embodiment G        or H. The host cell may be chosen from eukaryotic or prokaryotic        systems, such as for example bacterial cells, (Gram negative or        Gram positive), yeast cells, animal cells (such as Chinese        hamster ovary (CHO) cells), plant cells, and/or insect cells        using baculovirus vectors. In some embodiments, the host cells        for expression of the polypeptides include, and are not limited        to, those taught in U.S. Pat. Nos. 6,319,691, 6,277,375,        5,643,570, or 5,565,335, each of which is incorporated by        reference in its entirety, including all references cited within        each respective patent;

    -   I) novel compositions comprising a pharmaceutically acceptable        carrier and a polynucleotide according to embodiments A or B;

    -   J) methods of inducing an immune response or protective immune        response in an individual comprising the administration of a        composition comprising a polynucleotide according to embodiments        A and/or B and a pharmaceutically acceptable carrier in an        amount sufficient to induce an immune response;

    -   K) the method according to embodiment J, further comprising the        administration of: 1) a viral vector comprising a polynucleotide        according to embodiment A and/or B (or composition comprising        the viral vector); and/or 2) a polypeptide antigen (or        composition thereof) of the invention; in a preferred        embodiment, the antigen is the polypeptide that is encoded by        the polynucleotide administered as the polynucleotide vaccine.        As a particularly preferred embodiment, the polypeptide antigen        is administered as a booster subsequent to the initial        administration of the polynucleotide vaccine. Exemplary viral        vectors suitable for use in this embodiment include, but are not        limited to, poxvirus such as vaccinia virus, avipox virus,        fowlpox virus, a highly attenuated vaccinia virus (such as        Ankara or MVA [Modified Vaccinia Ankara]), retrovirus,        adenovirus, baculovirus and the like. In a preferred embodiment,        the viral vector is Ankara or MVA;

    -   L) compositions comprising the polynucleotides of embodiments A,        B, or F inserted into nucleic acid vaccine vectors (plasmids) or        viral vectors and, optionally, a pharmaceutically acceptable        carrier, e.g., saline;

    -   M) one or more isolated polypeptides comprising:        -   a) a polypeptide encoded by a polynucleotide sequence            according to embodiment A(a);        -   b) a variant polypeptide encoded by a polynucleotide            sequence having at least about 20% to 99.99% identity to a            polynucleotide according to embodiment A(a);        -   c) a fragment of a polypeptide or a variant polypeptide,            wherein said fragment or variant has substantially the same            serologic reactivity or substantially the same T-cell            reactivity as the native polypeptide (e.g., those            polypeptides set forth in SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8,            9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,            24, 25, 26, 27 and Tables 2, 3, 4, 5 or 6);        -   d) a polypeptide sequence provided in Tables 2, 3, 4, 5 or 6            or selected from the group consisting of SEQ ID NO: NO: 1,            2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,            19, 20, 21, 22, 23, 24, 25, 26, and 27;        -   e) a variant polypeptide having at least about 20% to 99.99%            identity to a polypeptide provided in Tables 2, 3, 4, 5 or 6            or selected from the group consisting of SEQ ID NO: NO: 1,            2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,            19, 20, 21, 22, 23, 24, 25, 26, and 27;        -   f) a polypeptide (epitope) set forth in Table 2, 3, 4, 5 or            6; or        -   g) a multi-epitope construct: 1) comprising at least one            epitope set forth in Table 2, 3, 4, 5 or 6; 2) comprising a            polypeptide selected from the group consisting of SEQ ID NO:            NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,            17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27 and at least            one epitope set forth in Tables 2, 3, 4, 5 and/or 6; or 3)            comprising and at least one epitope set forth in Tables 2,            3, 4, 5 and/or 6 and one or more polypeptide selected from            the group consisting of SEQ ID NO: NO: 1, 2, 3, 4, 5, 6, 7,            8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,            23, 24, 25, 26, and 27;

    -   N) a polypeptide epitope according to embodiment M(f), wherein        the polypeptide epitope is a CTL-inducing peptides of about 13        residues or less in length, preferably between about 8 and about        11 residues (e.g., 8, 9, 10 or all residues), and more        preferably 9 or 10 residues;

    -   O) a polypeptide epitope according to embodiment M(f), wherein        the polypeptide epitope is a HTL-inducing peptide of less than        about 50 residues, preferably, between about 6 and about 30        residues, more preferably, between about 12 and 25 residues        (e.g., 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25        residues), and most preferably, between about 15 and 20 residues        (e.g., 15, 16, 17, 18, 19, or 20 residues);

    -   P) methods for eliciting an immune response in an individual        comprising the administration of compositions comprising        polypeptides according to embodiment M or N to an individual in        amounts sufficient to induce an immune response in the        individual;

    -   Q) a composition comprising a pharmaceutically acceptable        carrier and a polypeptide according to embodiment M or N, that        can, optionally, contain an adjuvant;

    -   R) diagnostic assays based upon Western blot formats, or        standard immunoassays known to the skilled artisan, comprising        contacting a biological sample obtained from an individual with        a polypeptide according to the embodiments M or N and detecting        the formation of an antibody-antigen complex or detecting the        stimulation of T-cells obtained from the individual (for        example, as set forth in the Examples herein);

    -   S) a “multi-epitope construct” comprising: 1) polynucleotides        that encode multiple polypeptide epitopes (of any length) that        can bind to one or more molecules functioning in the immune        system; or 2) polypeptides comprising multiple polypeptide        epitopes that can bind to one or more molecules functioning in        the immune system. Some embodiments provide for “multi-epitope        constructs” that comprise a combination or series of different        epitopes, optionally connected by “flanking” residues.        “Multi-epitope constructs” can include the full length        polypeptides from which the epitopes are obtained (e.g., the        polypeptides of SEQ ID NOs: 1-27);

    -   T) a multi-epitope construct according to embodiment S, wherein        the epitopes used in the formation of the multi-epitope        construct are selected from those set forth in Table 2, Table,        3, Table 4, Table 5, and Table 6;

    -   U) a multi-epitope construct according to embodiments S or T        that is of “high affinity” or “intermediate affinity”;

    -   V) a multi-epitope construct according to embodiments S, T, or U        that comprises five or more, ten or more, fifteen or more,        twenty or more, or twenty-five or more epitopes. Other        embodiments provide multi-epitope constructs that comprise at        least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,        21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36,        37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52,        53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68,        69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84,        85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99        epitopes;

    -   W) a multi-epitope construct according to embodiments S, T, U,        or V wherein: a) all of the epitopes in a multi-epitope        construct are from one organism (e.g., the epitopes are obtained        from P. falciparum); or b) or the multi-epitope construct        includes epitopes present in two or more different organisms        (e.g., some epitopes from P. falciparum and some epitopes from        another organism). Additionally, the same epitope may be present        in a multi-epitope construct at more than one location in the        construct. In some embodiments, novel epitopes of the subject        invention may be linked to known epitopes of an organism        (e.g., P. falciparum or another organism);

    -   X) a multi-epitope construct according to embodiments S, T, U,        V, or W, wherein the individual epitopes interact with an        antigen binding site of an antibody molecule or fragment        thereof, a class I HLA, a T-cell receptor, and/or a class II HLA        molecule;

    -   Y) a multi-epitope construct according to embodiments S, T, U,        V, W, or X, wherein the construct further comprises, optionally,        1 to 5 “flanking” or “linking” residues positioned next to one        or more epitopes;

    -   Z) a multi-epitope construct according to embodiments S, T, U,        V, W, X, or Y that has, optionally, been “optimized”;

    -   AA) an isolated antibody or fragment thereof that specifically        binds to a polypeptide as set forth in embodiments M or N;

    -   BB) a viral vector comprising a polynucleotide according to        embodiment A or B. Exemplary viral vectors suitable for use in        this embodiment include, but are not limited to, poxvirus such        as vaccinia virus, avipox virus, fowlpox virus, a highly        attenuated vaccinia virus (such as Ankara or MVA [Modified        Vaccinia Ankara]), retrovirus, adenovirus, baculovirus and the        like. In a preferred embodiment, the viral vector is Ankara or        MVA; and/or

    -   CC) a viral vector according to embodiment BB, wherein the viral        vector further comprises nucleic acids encoding        immunostimulatory molecules such as IL-1, IL-2, IL-3, IL-4,        IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-15, II-16, II-18,        IL-23, IL-24, erythropoietin, G-CSF, M-CSF, platelet derived        growth factor (PDGF), MSF, FLT-3 ligand, EGF, fibroblast growth        factor (FGF; e.g., aFGF (FGF-1), bFGF (FGF-2), FGF-3, FGF-4,        FGF-5, FGF-6, or FGF-7), insulin-like growth factors (e.g.,        IGF-1, IGF-2); vascular endothelial growth factor (VEGF);        interferons (e.g., IFN-γ, IFN-α. IFN-β); leukemia inhibitory        factor (LIF); ciliary neurotrophic factor (CNTF); oncostatin M;        stem cell factor (SCF); transforming growth factors (e.g.,        TGF-a, TGF-β1, TGF-β1, TGF-β1), or chemokines (such as, but not        limited to, BCA-1/BLC-1, BRAK/Kec, CXCL16, CXCR3, ENA-78/LIX,        Eotaxin-1, Eotaxin-2/MPIF-2, Exodus-2/SLC,        Fractalkine/Neur7otactin, GROalpha/MGSA, HCC-1, I-TAC,        Lymphotactin/ATAC/SCM, MCP-1/MCAF, MCP-3, MCP-4, MDC/STCP-1,        ABCD-1, MIP-1α, MIP-β3, MIP-2α/GROβ, MIP-3α/Exodus/LARC,        MIP-3β/Exodus-3/ELC, MIP-4/PARC/DC-CK1, PF-4, RANTES, SDF1α,        TARC, or TECK).

BRIEF DESCRIPTION OF DRAWINGS AND TABLES

Table 1 presents a summary of immune reactivities of a panel of 27 novelantigens and four known antigens.

Tables 2-6 provide peptide epitopes of P. falciparum.

BRIEF DESCRIPTION OF SEQUENCES

Sequence ID NOs: 1-27 are amino acid sequences of novel malariaantigens.

DETAILED DISCLOSURE

The subject invention provides isolated and/or purified novel P.falciparum polynucleotides and fragments of these novel polynucleotides.Thus, the present invention provides isolated and/or purifiedpolynucleotide sequences comprising:

-   -   a polynucleotide sequence encoding a polypeptide sequence        selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5,        6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,        23, 24, 25, 26, and 27;    -   a complementary polynucleotide sequence to a polynucleotide        sequence encoding a polypeptide sequence selected from the group        consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,        13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27;    -   a polynucleotide sequence having at least about 20% to 99.99%        identity to a polynucleotide sequence of (a) or (b);    -   a fragment of a polynucleotide sequence according to (a) or (b);    -   a polynucleotide sequence encoding a polypeptide as set forth in        Table 2, 3, 4, 5 or 6 or a polynucleotide sequence encoding a        polypeptide selected from the group consisting of SEQ ID NO: 1,        2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,        20, 21, 22, 23, 24, 25, 26, and 27;    -   a polynucleotide sequence encoding variant of a polypeptide        (e.g., a variant polypeptide) selected from the group consisting        of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,        16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27;    -   a polynucleotide sequence encoding a polypeptide fragment of a        polypeptide selected from the group consisting of SEQ ID NO: 1,        2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,        20, 21, 22, 23, 24, 25, 26, and 27, wherein the fragment has        substantially the same serologic reactivity as the native        polypeptide or substantially the same T-cell reactivity as the        native polypeptide or fragment;    -   a polynucleotide sequence encoding a fragment of a variant        polypeptide of a polypeptide selected from the group consisting        of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,        16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27, wherein the        fragment of the variant polypeptide has substantially the same        serologic activity as the native polypeptide or substantially        the same T-cell reactivity as the native polypeptide or        fragment; or    -   a polynucleotide sequence encoding a multi-epitope construct.

“Nucleotide sequence”, “polynucleotide” or “nucleic acid” can be usedinterchangeably and are understood to mean, according to the presentinvention, either a double-stranded DNA, a single-stranded DNA orproducts of transcription of the said DNAs (e.g., RNA molecules). Itshould also be understood that the present invention does not relate togenomic polynucleotide sequences of P. falciparum in their naturalenvironment or natural state. The nucleic acid, polynucleotide, ornucleotide sequences of the invention have been isolated, purified (orpartially purified), by separation methods including, but not limitedto, ion-exchange chromatography, molecular size exclusionchromatography, affinity chromatography, or by genetic engineeringmethods such as amplification, cloning, subcloning or chemicalsynthesis.

A homologous polynucleotide or polypeptide sequence, for the purposes ofthe present invention, encompasses a sequence having a percentageidentity with the polynucleotide or polypeptide sequences, set forthherein, of between at least (or at least about) 20.00% to 99.99%(inclusive). The aforementioned range of percent identity is to he takenas including, and providing written description and support for, anyfractional percentage, in intervals of 0.01%, between 20.00% and, up to,including 99.99%. These percentages are purely statistical anddifferences between two nucleic acid sequences can be distributedrandomly and over the entire sequence length.

In various embodiments, homologous sequences can exhibit a percentidentity of 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52,53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70,71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88,89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99 percent with the sequencesof the instant invention. Typically, the percent identity is calculatedwith reference to the full length, native, and/or naturally occurringpolypeptide or polynucleotide (e.g., those polypeptides set forth in SEQID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,19, 20, 21, 22, 23, 24, 25, 26, 27 or those set forth in SEQ IDNOs:28-81)). The terms “identical” or percent “identity”, in the contextof two or more polynucleotide or polypeptide sequences, refer to two ormore sequences or subsequences that are the same or have a specifiedpercentage of amino acid residues that are the same, when compared andaligned for maximum correspondence over a comparison window, as measuredusing a sequence comparison algorithm or by manual alignment and visualinspection. Preferably, such a substitution is made in accordance withanaloging principles set forth, e.g., in co-pending U.S. Ser. No.09/260,714 filed Mar. 1, 1999 and Ser. No. 09/226,775, filed Jan. 6,1999 and PCT application number PCT/US00/19774 each of which is herebyincorporated by reference in its entirety.

Both protein and nucleic acid sequence homologies may be evaluated usingany of the variety of sequence comparison algorithms and programs knownin the art. Such algorithms and programs include, but are by no meanslimited to, TBLASTN, BLASTP, FASTA, TFASTA, and CLUSTALW (Pearson andLipman, 1988, Proc. Natl. Acad. Sci. USA 85(8):2444-2448; Altschul etal., 1990, J. Mol. Biol. 215(3):403-410; Thompson et al., 1994, NucleicAcids Res. 22(2):4673-4680; Higgins et al., 1996, Methods Enzymol.266:383-402; Altschul et al., 1990, J. Mol. Biol. 215(3):403-410;Altschul et al., 1993, Nature Genetics 3:266-272). Sequence comparisonsare, typically, conducted using default parameters provided by thevendor or using those parameters set forth in the above-identifiedreferences, which are hereby incorporated by reference in theirentireties. A “complementary” polynucleotide sequence, as used herein,generally refers to a sequence arising from the hydrogen bonding betweena particular purine and a particular pyrimidine in double-strandednucleic acid molecules (DNA-DNA, DNA-RNA, or RNA-RNA). The majorspecific pairings are guanine with cytosine and adenine with thymine oruracil. A “complementary” polynucleotide sequence may also be referredto as an “antisense” polynucleotide sequence or an “antisense” sequence.

Sequence homology and sequence identity can also be determined byhybridization studies under high stringency, intermediate stringency,and/or low stringency. Various degrees of stringency of hybridizationcan be employed. The more severe the conditions, the greater thecomplementarity that is required for duplex formation. Severity ofconditions can be controlled by temperature, probe concentration, probelength, ionic strength, time, and the like. Preferably, hybridization isconducted under low, intermediate, or high stringency conditions bytechniques well known in the art, as described, for example, in Keller,G. H., M. M. Manak [1987] DNA Probes, Stockton Press, New York, N.Y.,pp. 169-170.

For example, hybridization of immobilized. DNA on Southern blots with³²P-labeled gene-specific probes can be performed by standard methods(Maniatis et al. [1982] Molecular Cloning: A Laboratory Manual, ColdSpring Harbor Laboratory, New York). In general, hybridization andsubsequent washes can be carried out under intermediate to highstringency conditions that allow for detection of target sequences withhomology to the exemplified polynucleotide sequence. For double-strandedDNA gene probes, hybridization can be carried out overnight at 20-25° C.below the melting temperature (T_(m)) of the DNA hybrid in 6×SSPE,5×Denhardt's solution, 0.1% SDS, 0.1 mg/ml denatured DNA. The meltingtemperature is described by the following formula (Beltz et al. [1983]Methods of Enzymology, R. Wu, L. Grossman and K. Moldave [eds.] AcademicPress, New York 100:266-285).

Tm=81.5° C.+16.6 Log [Na⁺]0.41(% G+C)−0.61(% formamide)−600/length ofduplex in base pairs.

Washes are typically carried out as follows:

-   -   (1) twice at room temperature for 15 minutes in 1×SSPE, 0.1% SDS        (low stringency wash);    -   (2) once at T_(m)−20° C. for 15 minutes in 0.2×SSPE, 0.1% SDS        (intermediate stringency wash).

For oligonucleotide probes, hybridization can be carried out overnightat 10-20° C. below the melting temperature (T_(m)) of the hybrid in6×SSPE, 5×Denhardt's solution, 0.1% SDS, 0.1 mg/ml denatured DNA. T_(m)for oligonucleotide probes can be determined by the following formula:

T _(m) (° C.)=2(number T/A base pairs)⁺4(number G/C base pairs) (Suggset al. [1981] ICN-UCLA Symp. Dev. Biol. Using Purified Genes, D. D.Brown [ed.], Academic Press, New York, 23:683-693).

Washes can be carried out as follows:

-   -   (1) twice at room temperature for 15 minutes 1×SSPE, 0.1% SDS        (low stringency wash);    -   2) once at the hybridization temperature for 15 minutes in        1×SSPE, 0.1% SDS (intermediate stringency wash).

In general, salt and/or temperature can be altered to change stringency.With a labeled DNA fragment >70 or so bases in length, the followingconditions can be used:

Low: 1 or 2×SSPE, room temperature

Low: 1 or 2×SSPE, 42° C.

Intermediate: 0.2× or 1×SSPE, 65° C.

High: 0.1×SSPE, 65° C.

By way of another non-limiting example, procedures using conditions ofhigh stringency can also be performed as follows: Pre-hybridization offilters containing DNA is carried out for 8 h to overnight at 65° C. inbuffer composed of 6×SSC, 50 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.02% PVP,0.02% Ficoll, 0.02% BSA, and 500 μg/ml denatured salmon sperm DNA.Filters are hybridized for 48 h at 65° C., the preferred hybridizationtemperature, in pre-hybridization mixture containing 100 μg/ml denaturedsalmon sperm DNA and 5-20×10⁶ cpm of ³²P-labeled probe. Alternatively,the hybridization step can be performed at 65° C. in the presence of SSCbuffer, 1×SSC corresponding to 0.15M NaCl and 0.05 M Na citrate.Subsequently, filter washes can be done at 37° C. for 1 h in a solutioncontaining 2×SSC, 0.01% PVP, 0.01% Ficoll, and 0.01% BSA, followed by awash in 0.1×SSC at 50° C. for 45 min. Alternatively, filter washes canbe performed in a solution containing 2×SSC and 0.1% SDS, or 0.5×SSC and0.1% SDS, or 0.1×SSC and 0.1% SDS at 68° C. for 15 minute intervals.Following the wash steps, the hybridized probes are detectable byautoradiography. Other conditions of high stringency which may be usedare well known in the art and as cited in Sambrook et al., 1989,Molecular Cloning, A Laboratory Manual, Second Edition, Cold SpringHarbor Press, N.Y., pp. 9.47-9.57; and Ausubel et al., 1989, CurrentProtocols in Molecular Biology, Green Publishing Associates and WileyInterscience, N.Y. are incorporated herein in their entirety.

Another non-limiting example of procedures using conditions ofintermediate stringency are as follows: Filters containing DNA arepre-hybridized, and then hybridized at a temperature of 60° C. in thepresence of a 5×SSC buffer and labeled probe. Subsequently, filterswashes are performed in a solution containing 2×SSC at 50° C. and thehybridized probes are detectable by autoradiography. Other conditions ofintermediate stringency which may he used are well known in the art andas cited in Sambrook et al., 1989, Molecular Cloning, A LaboratoryManual, Second Edition, Cold Spring Harbor Press, N.Y., pp. 9.47-9.57;and Ausubel et al., 1989, Current Protocols in Molecular Biology, GreenPublishing Associates and Wiley Interscience, N.Y. are incorporatedherein in their entirety.

Duplex formation and stability depend on substantial complementaritybetween the two strands of a hybrid and, as noted above, a certaindegree of mismatch can be tolerated. Therefore, the probe sequences ofthe subject invention include mutations (both single and multiple),deletions, insertions of the described sequences, and combinationsthereof, wherein said mutations, insertions and deletions permitformation of stable hybrids with the target polynucleotide of interest.Mutations, insertions and deletions can be produced in a givenpolynucleotide sequence in many ways, and these methods are known to anordinarily skilled artisan. Other methods may become known in thefuture. It is also well known in the art that restriction enzymes can beused to obtain functional fragments of the subject DNA sequences. Forexample, Bal31 exonuclease can be conveniently used for time-controlledlimited digestion of DNA (commonly referred to as “erase-a-base”procedures). See, for example, Maniatis et al. [1982] Molecular Cloning:A Laboratory Manual, Cold Spring Harbor Laboratory, New York; Wei et al.[1983] J. Biol. Chem. 258:13006-13512.

The present invention further comprises fragments of the polynucleotidesequences of the instant invention. Representative fragments of thepolynucleotide sequences according to the invention will be understoodto mean any nucleotide fragment having at least 8 successivenucleotides, preferably at least 12 successive nucleotides, and stillmore preferably at least 15 or at least 20 successive nucleotides of thesequence from which it is derived. The upper limit for such fragments isthe total number of polynucleotides found in the full length sequence(or, in certain embodiments, of the full length open reading frame (ORF)identified herein).

In some embodiments, the subject invention includes those fragmentscapable of hybridizing under various conditions of stringency conditions(e.g., high or intermediate or low stringency) with a nucleotidesequence according to the invention; fragments that hybridize with anucleotide sequence of the subject invention can be, optionally, labeledas set forth below.

Other embodiments provide for nucleic acid fragments corresponding tonucleotide sequences comprising full, or partial, open reading frames(ORF sequences). Also within the scope of the invention are thosepolynucleotide fragments encoding polypeptides reactive with antibodiesfound in the serum of individuals infected with P. falciparum. Fragmentsaccording to the subject invention can be obtained, for example, byspecific amplification (e.g., PCR amplification), digestion withrestriction enzymes, of nucleotide sequences according to the invention.Such methodologies are well-known in the art and are taught, forexample, by Sambrook et al., 1989. Nucleic acid fragments according tothe invention can also be obtained by chemical synthesis according tomethods well known to persons skilled in the art.

The subject invention also provides nucleic acid based methods for theidentification of the presence of an organism in a sample. In thesevaried embodiments, the invention provides for the detection of nucleicacids in a sample comprising contacting a sample with a nucleic acid(polynucleotide) of the subject invention (such as an RNA, mRNA, DNA,cDNA, or other nucleic acid). In a preferred embodiment, thepolynucleotide is a probe that is, optionally, labeled and used in thedetection system. Many methods for detection of nucleic acids exist andany suitable method for detection is encompassed by the instantinvention. Typical assay formats utilizing nucleic acid hybridizationincludes, and are not limited to, 1) nuclear run-on assay, 2) slot blotassay, 3) northern blot assay (Alwine, et al. Proc. Natl. Acad. Sci.74:5350), 4) magnetic particle separation, 5) nucleic Acid or DNA chips,6) reverse Northern blot assay, 7) dot blot assay, 8) in situhybridization, 9) RNase protection assay (Melton, et al. Nuc. Acids Res.12:7035 and as described in the 1998 catalog of Ambion, Inc., Austin,Tex.), 10) ligase chain reaction, 11) polymerase chain reaction (PCR),12) reverse transcriptase (RT)-PCR (Berchtold, et al. Nuc. Acids. Res.17:453), 13) differential display RT-PCR (DDRT-PCR) or other suitablecombinations of techniques and assays. Labels suitable for use in thesedetection methodologies include, and are not limited to 1) radioactivelabels, 2) enzyme labels, 3) chemiluminescent labels, 4) fluorescentlabels, 5) magnetic labels, or other suitable labels, including thoseset forth below. These methodologies and labels are well known in theart and widely available to the skilled artisan. Likewise, methods ofincorporating labels into the nucleic acids are also well known to theskilled artisan.

Thus, the subject invention also provides detection probes (e.g.,fragments of the disclosed polynucleotide sequences) for hybridizationwith a target sequence or the amplicon generated from the targetsequence. Such a detection probe will advantageously have as sequence asequence of at least 8, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80,85, 90, 95, or 100 nucleotides. Labeled probes or primers are labeledwith a radioactive compound or with another type of label as set forthabove. Alternatively, non-labeled nucleotide sequences may be useddirectly as probes or primers; however, the sequences are generallylabeled with a radioactive element (³²P, ³⁵ _(S,) ³H, ¹²⁵I) orw_(i)t_(h) a molecule such as biotin, acetylaminofluorene, digoxigenin,5-bromo-deoxyuridine, or fluorescein to provide probes that can be usedin numerous applications.

The polynucleotide sequences according to the invention may also he usedin analytical systems, such as DNA chips. DNA chips and their uses arewell known in the art and (see for example, U.S. Pat. Nos. 5,561,071;5,753,439; 6,214,545; Schena et al., BioEssays, 1996, 18:427-431;Bianchi et al., Clin. Diagn. Virol., 1997, 8:199-208; each of which ishereby incorporated by reference in their entireties) and/or areprovided by commercial vendors such as Affymetrix, Inc. (Santa Clara,Calif.). In addition, the nucleic acid sequences of the subjectinvention can be used as molecular weight markers in nucleic acidanalysis procedures.

The subject invention also provides for modified nucleotide sequences.Modified nucleic acid sequences will be understood to mean anynucleotide sequence that has been modified, according to techniques wellknown to persons skilled in the art, and exhibiting modifications inrelation to the native, naturally occurring nucleotide sequences. Onenon-limiting example of a “modified” nucleotide sequences includesmutations in regulatory and/or promoter sequences of a polynucleotidesequence that result in a modification of the level of expression of thepolypeptide. A “modified” nucleotide sequence will also be understood tomean any nucleotide sequence encoding a “modified” polypeptide asdefined below.

Another aspect of the invention provides vectors for the cloning and/orthe expression of a polynucleotide sequence taught herein. Vectors ofthis invention, including vaccine vectors, can also comprise elementsnecessary to allow the expression and/or the secretion of the saidnucleotide sequences in a given host cell. The vector can contain apromoter, signals for initiation and for termination of translation, aswell as appropriate regions for regulation of transcription. In certainembodiments, the vectors can be stably maintained in the host cell andcan, optionally, contain signal sequences directing the secretion oftranslated protein. These different elements are chosen according to thehost cell used. Vectors can integrate into the host genome or,optionally, be autonomously-replicating vectors.

The subject invention also provides for the expression of a polypeptide,peptide, derivative, or variant encoded by a polynucleotide sequencedisclosed herein comprising the culture of an organism transformed witha polynucleotide of the subject invention under conditions that allowfor the expression of the polypeptide, peptide, derivative, or analogand, optionally, recovering the expressed polypeptide, peptide,derivative, or analog.

The disclosed polynucleotide sequences can also be regulated by a secondnucleic acid sequence so that the protein or peptide is expressed in ahost transformed with the recombinant DNA molecule. For example,expression of a protein or peptide may be controlled by anypromoter/enhancer element known in the art. Promoters which may be usedto control expression include, but are not limited to, the CMV-IEpromoter, the SV40 early promoter region (Bernoist and Chambon, 1981,Nature 290:304-310), the promoter contained in the 3′ long terminalrepeat of Rous sarcoma virus (Yamamoto, et al., 1980, Cell 22:787-797),the herpes simplex thymidine kinase promoter (Wagner et al., 1981, Proc.Natl. Acad. Sci. U.S.A. 78:1441-1445), the regulatory sequences of themetallothionein gene (Brinster et al., 1982, Nature 296:39-42);prokaryotic vectors containing promoters such as the β-lactamasepromoter (Villa-Kamaroff, et al., 1978, Proc. Natl. Acad. Sci. U.S.A.75:3727-3731), or the tac promoter (DeBoer, et al., 1983, Proc. Natl.Acad. Sci. U.S.A. 80:21-25); see also “Useful proteins from recombinantbacteria” in Scientific American, 1980, 242:74-94; plant expressionvectors comprising the nopaline synthetase promoter region(Herrera-Estrella et al., 1983, Nature 303:209-213) or the cauliflowermosaic virus 35S RNA promoter (Gardner, et al., 1981, Nucl. Acids Res.9:2871), and the promoter of the photosynthetic enzyme ribulosebiphosphate carboxylase (Herrera-Estrella et al., 1984, Nature310:115-120); promoter elements from yeast or fungi such as the Gal 4promoter, the ADC (alcohol dehydrogenase) promoter, PGK (phosphoglycerolkinase) promoter, and/or the alkaline phosphatase promoter.

The vectors according to the invention are, for example, vectors ofplasmid or viral origin. In a specific embodiment, a vector is used thatcomprises a promoter operably linked to a protein or peptide-encodingnucleic acid sequence contained within the disclosed polynucleotidesequences, one or more origins of replication, and, optionally, one ormore selectable markers (e.g., an antibiotic resistance gene).Expression vectors comprise regulatory sequences that control geneexpression, including gene expression in a desired host cell. Exemplaryvectors for the expression of the polypeptides of the invention includethe pET-type plasmid vectors (Promega) or pBAD plasmid vectors(Invitrogen) or those provided in the examples below. Furthermore, thevectors according to the invention are useful for transforming hostcells so as to clone or express the polynucleotide sequences of theinvention.

The invention also encompasses the host cells transformed by a vectoraccording to the invention. These cells may be obtained by introducinginto host cells a nucleotide sequence inserted into a vector as definedabove, and then culturing the said cells under conditions allowing thereplication and/or the expression of the polynucleotide sequences of thesubject invention.

The host cell may be chosen from eukaryotic or prokaryotic systems, suchas for example bacterial cells, (Gram negative or Gram positive), yeastcells (for example, Saccharomyces cereviseae or Pichia pastoris), animalcells (such as Chinese hamster ovary (CHO) cells), plant cells, and/orinsect cells using baculovirus vectors. In some embodiments, the hostcells for expression of the polypeptides include, and are not limitedto, those taught in U.S. Pat. Nos. 6,319,691, 6,277,375, 5,643,570, or5,565,335, each of which is incorporated by reference in its entirety,including all references cited within each respective patent.

Furthermore, a host cell strain may be chosen which modulates theexpression of the inserted sequences, or modifies and processes the geneproduct in the specific fashion desired. Expression from certainpromoters can be elevated in the presence of certain inducers; thus,expression of the genetically engineered polypeptide may be controlled.Furthermore, different host cells have characteristic and specificmechanisms for the translational and post-translational processing andmodification (e.g., glycosylation, phosphorylation) of proteins.Appropriate cell lines or host systems can be chosen to ensure thedesired modification and processing of the foreign protein expressed.For example, expression in a bacterial system can be used to produce anunglycosylated core protein product. Expression in yeast will produce aglycosylated product. Expression in mammalian cells can be used toensure “native” glycosylation of a heterologous protein. Furthermore,different vector/host expression systems may effect processing reactionsto different extents.

The subject invention also concerns novel compositions that can beemployed to elicit an immune response or a protective immune response.In this aspect of the invention, an amount of a composition comprisingrecombinant DNA or mRNA encoding an polynucleotide of the subjectinvention sufficient to elicit an immune response or protective immuneresponse is administered to an individual. Signal sequences may bedeleted from the nucleic acid encoding an antigen of interest and theindividual may be monitored for the induction of an immune responseaccording to methods known in the art. A “protective immune response” or“therapeutic immune response” refers to a CTL (or CD8⁺ T cell) and/or anHTL (or CD4⁺ T cell) response to an antigen that, in some way, preventsor at least partially arrests disease symptoms, side effects orprogression. The immune response may also include an antibody responsethat has been facilitated by the stimulation of helper T cells.

In another embodiment, the subject invention further comprises theadministration of polynucleotide vaccines in conjunction with apolypeptide antigen, or composition thereof, of the invention. In apreferred embodiment, the antigen is the polypeptide that is encoded bythe polynucleotide administered as the polynucleotide vaccine. As aparticularly preferred embodiment, the polypeptide antigen isadministered as a booster subsequent to the initial administration ofthe polynucleotide vaccine.

A further embodiment of the subject invention provides for the inductionof an immune response to the novel Plasmodium falciparum antigensdisclosed herein (see, for example, the antigens and peptides set forthin the Tables and Sequence Listing attached hereto) using a“prime-boost” vaccination regimen known to those skilled in the art. Inthis aspect of the invention, a DNA vaccine is administered to anindividual in an amount sufficient to “prime” the immune response of theindividual, provided that the DNA vaccine comprises nucleic acidsencoding the antigens, multi-epitope constructs, and/or peptide antigensset forth herein. The immune response of the individual is then“boosted” via the administration of: 1) one or a combination of: apeptide, polypeptide, and/or full length polypeptide antigen (e.g., SEQID NOs: 1-27) of the subject invention (optionally in conjunction with aimmunostimulatory molecule and/or an adjuvant); or 2) a viral vectorthat contains nucleic acid encoding one, or more, of the same or,optionally, different, antigens, multi-epitope constructs, and/orpeptide antigens set forth in the Tables or Sequence Listing of thesubject application. In some alternative embodiments of the invention, agene encoding an immunostimulatory molecule may be incorporated into theviral vector used to “boost the immune response of the individual.Exemplary immunostimulatory molecules include, and are not limited to,IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, 1L-9, IL-10, IL-11,IL-15, 11-16, 11-18, IL-23, IL-24, erythropoietin, G-CSF, M-CSF,platelet derived growth factor (PDGF), MSF, FLT-3 ligand, EGF,fibroblast growth factor (FGF; e.g., aFGF (FGF-1), bFGF (FGF-2), FGF-3,FGF-4, FGF-5, FGF-6, or FGF-7), insulin-like growth factors (e.g.,IGF-1, IGF-2); vascular endothelial growth factor (VEGF); interferons(e.g., IFN-γ, IFN-α, IFN-β); leukemia inhibitory factor (LIF); ciliaryneurotrophic factor (CNTF); oncostatin M; stem cell factor (SCF);transforming growth factors (e.g., TGF-a, TGF-β1, TGF-β1, TGF-β1), orchemokines (such as, but not limited to, BCA-1/BLC-1, BRAK/Kec, CXCL16,CXCR3, ENA-78/LIX, Eotaxin-1, Eotaxin-2/MPIF-2, Exodus-2/SLC,Fractalkine/Neurotactin, GROalpha/MGSA, HCC-1, I-TAC,Lymphotactin/ATAC/SCM, MCP-1/MCAF, MCP-3, MCP-4, MDC/STCP-1, ABCD-1,MIP-1α, MIP-1β, MIP-2α/GROβ, MIP-3α/Exodus/LARC, MIP-3β/Exodus-3/ELC,MIP-4/PARC/DC-CK1, PF-4, RANTES, SDF1α, TARC, or TECK). Genes encodingthese immunostimulatory molecules are known to those skilled in the artand coding sequences may be obtained from a variety of sources,including various patents databases, publicly available databases (suchas the nucleic acid and protein databases found at the National Libraryof Medicine or the European Molecular Biology Laboratory), thescientific literature, or scientific literature cited in catalogsproduced by companies such as Genzyme, Inc., R&D Systems, Inc, orInvivoGen, Inc. [see, for example, the 1995 Cytokine Research Productscatalog, Genzyme Diagnostics, Genzyme Corporation, Cambridge Mass.; 2002or 1995 Catalog of R&D Systems, Inc (Minneapolis, Minn.); or 2002Catalog of InvivoGen, Inc (San Diego, Calif.) each of which isincorporated by reference in its entirety, including all referencescited therein].

Methods of introducing DNA vaccines into individuals are well-known tothe skilled artisan. For example, DNA can be injected into skeletalmuscle or other somatic tissues (e.g., intramuscular injection).Cationic liposomes or biolistic devices, such as a gene gun, can be usedto deliver DNA vaccines. Alternatively, iontophoresis and other meansfor transdermal transmission can be used for the introduction of DNAvaccines into an individual.

Viral vectors for use in the subject invention can have a portion of theviral genome deleted to introduce new genes without destroyinginfectivity of the virus. The viral vector of the present invention is,typically, a non-pathogenic virus. At the option of the practitioner,the viral vector can be selected so as to infect a specific cell type,such as professional antigen presenting cells (e.g., macrophage ordendritic cells). Alternatively, a viral vector can be selected that isable to infect any cell in the individual. Exemplary viral vectorssuitable for use in the present invention include, but are not limitedto poxvirus such as vaccinia virus, avipox virus, fowlpox virus, ahighly attenuated vaccinia virus (such as Ankara or MVA [ModifiedVaccinia Ankara]), retrovirus, adenovirus, baculovirus and the like. Ina preferred embodiment, the viral vector is Ankara or MVA. Generalstrategies for construction of vaccinia virus expression vectors areknown in the art (see, for example, Smith and Moss Bio TechniquesNovember/December, 306-312, 1984; U.S. Pat. No. 4,738,846 (herebyincorporated by reference in its entirety). Sutter and Moss (Proc.Nat'l. Acad. Sci U.S.A. 89:10847-10851, 1992) and Sutter et al.(Vaccine, 12(11):1032-40, 1994) disclose the construction and use as avector, a non-replicating recombinant Ankara virus (MVA) which can beused as a viral vector in the present invention. Other versions of theModified Vaccinia Ankara strain can also be used in the practice of thesubject invention (such as the MVA-BN strain produced by Bavarian NordicS/A (Copenhagen, Denmark).

Compositions comprising the subject polynucleotides can includeappropriate nucleic acid vaccine vectors (plasmids), which arecommercially available (e.g., Vical, San Diego, Calif.) or other nucleicacid vectors (plasmids), which are also commercially available (e.g.,Valenti, Burlingame, Calif.). Alternatively, compositions comprisingviral vectors and polynucleotides according to the subject invention areprovided by the subject invention. In addition, the compositions caninclude a pharmaceutically acceptable carrier, e.g., saline. Thepharmaceutically acceptable carriers are well known in the art and alsoare commercially available. For example, such acceptable carriers aredescribed in E. W. Martin's Remington's Pharmaceutical Science, MackPublishing Company, Easton, Pa.

The subject invention also provides one or more isolated polypeptidescomprising:

-   -   a) a polypeptide encoded by a polynucleotide sequence according        to embodiment A(a) (set forth above);    -   b) a variant polypeptide encoded by a polynucleotide sequence        having at least about 20% to 99.99% identity to a polynucleotide        according to embodiment A(a) (as set forth above);    -   c) a fragment of a polypeptide or a variant polypeptide, wherein        said fragment or variant has substantially the same serologic        reactivity or substantially the same T-cell reactivity as the        native polypeptide (e.g., those polypeptides set forth in SEQ ID        NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,        18, 19, 20, 21, 22, 23, 24, 25, 26, 27 and Table 2, 3, 4, 5 or        6);    -   d) a polypeptide sequence provided in Table 2, 3, 4, 5 or 6 or        selected from the group consisting of SEQ ID NO: NO: 1, 2, 3, 4,        5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,        22, 23, 24, 25, 26, and 27;    -   e) a variant polypeptide having at least about 20% to 99.99%        identity to a polypeptide provided in Table 2, 3, 4, 5 or 6 or        selected from the group consisting of SEQ ID NO: NO: 1, 2, 3, 4,        5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,        22, 23, 24, 25, 26, and 27;    -   f) a polypeptide (epitope) set forth in Table 2, 3, 4, 5 or 6;        or    -   g) a multi-epitope construct: 1) comprising at least one epitope        set forth in Table 2, 3, 4, 5 or 6; 2) comprising a polypeptide        selected from the group consisting of SEQ ID NO: NO: 1, 2, 3, 4,        5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,        22, 23, 24, 25, 26, and 27 and at least one epitope set forth in        Tables 2, 3, 4, 5 or 6; or 3) comprising and at least one        epitope set forth in Tables 2, 3, 4, 5 or 6 and one or more        polypeptide selected from the group consisting of SEQ ID NO: NO:        1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,        19, 20, 21, 22, 23, 24, 25, 26, and 27.

The term “peptide” may be used interchangeably with “oligopeptide” or“polypeptide” or “epitope” in the present specification to designate aseries of residues, typically L-amino acids, connected one to the other,typically by peptide bonds between the α-amino and carboxyl groups ofadjacent amino acids. The preferred CTL (or CD8⁺ T cell)-inducingpeptides of the invention are 13 residues or less in length and usuallyconsist of between about 8 and about 11 residues (e.g., 8, 9, 10 or 11residues), preferably 9 or 10 residues. The preferred HTL (or CD4⁺ Tcell)-inducing peptides are less than about 50 residues in length andusually consist of between about 6 and about 30 residues, more usuallybetween about 12 and 25 (e.g., 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,22, 23, 24 or 25), and often between about 15 and 20 residues (e.g., 15,16, 17, 18, 19 or 20).

According to the subject invention, a “fragment” is a polypeptide of atleast 3 consecutive, preferably 4 consecutive, and even more preferably5 consecutive amino acids. In some embodiments, the polypeptidefragments are reactive with antibodies found in the serum of anindividual. In other embodiments, a fragment is an “epitope” asdescribed supra. In the context of the instant invention, the termspolypeptide, peptide and protein can be used interchangeably; however,it should be understood that the invention does not relate to thepolypeptides in natural form, that is to say that they are not in theirnatural environment but that the polypeptides may have been isolated orobtained by purification from natural sources, obtained from host cellsprepared by genetic manipulation (e.g., the polypeptides, or fragmentsthereof, are recombinantly produced by host cells, or by chemicalsynthesis). Polypeptides according to the instant invention may alsocontain non-natural amino acids, as will be described below.

A “variant” or “modified” polypeptide (or polypeptide variant) is to beunderstood to designate polypeptides exhibiting, in relation to thenatural polypeptide, certain modifications. These modifications caninclude a deletion, addition, or substitution of at least one aminoacid, a truncation, an extension, a chimeric fusion, a mutation, orpolypeptides exhibiting post-translational modifications. Among thehomologous polypeptides, those whose amino acid sequences exhibitbetween at least (or at least about) 20.00% to 99.99% (inclusive)identity to the full length, native, or naturally occurring polypeptideare another aspect of the invention. The aforementioned range of percentidentity is to be taken as including, and providing written descriptionand support for, any fractional percentage, in intervals of 0.01%,between 20.00% and, up to, including 99.99%. These percentages arepurely statistical and differences between two polypeptide sequences canbe distributed randomly and over the entire sequence length.

Variant peptides (epitopes) can also be created by altering the presenceor absence of particular residues in these primary anchor positions.Such analogs are used to modulate the binding affinity of a peptidecomprising a particular motif or supermotif. The term “motif' refers tothe pattern of residues in a peptide of defined length, usually apeptide of from about 8 to about 13 amino acids for a class I HLA motif(e.g., 8, 9, 10, 11, 12 or 13 aa) and from about 6 to about 25 aminoacids for a class II HLA motif (e.g., 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or 25 amino acids), which isrecognized by a particular HLA molecule. Peptide motifs are typicallydifferent for each protein encoded by each human HLA allele and differin the pattern of the primary and secondary anchor residues. Optionally,variant peptides or polypeptides can also comprise one or moreheterologous polypeptide sequences (e.g., tags that facilitatepurification of the polypeptides of the invention (see, for example,U.S. Pat. No. 6,342,362, hereby incorporated by reference in itsentirety; Altendorf et al. [1999-WWW, 2000] “Structure and Function ofthe F_(o) Complex of the ATP Synthase from Escherichia Coli,” J. ofExperimental Biology 203:19-28, The Co. of Biologists, Ltd., G. B.;Baneyx [1999] “Recombinant Protein Expression in Escherichia coli,”Biotechnology 10:411-21, Elsevier Science Ltd.; Eihauer et al. [2001]“The FLAG™ Peptide, a Versatile Fusion Tag for the Purification ofRecombinant Proteins,” J. Biochem Biophys Methods 49:455-65; Jones etal. [1995] J. Chromatography 707:3-22; Jones et al. [1995] “CurrentTrends in Molecular Recognition and Bioseparation,” J. of ChromatographyA. 707:3-22, Elsevier Science B. V.; Margolin [2000] “Green FluorescentProtein as a Reporter for Macromolecular Localization in BacterialCells,” Methods 20:62-72, Academic Press; Puig et al. [2001] “The TandemAffinity Purification (TAP) Method: A General Procedure of ProteinComplex Purification,” Methods 24:218-29, Academic Press; Sassenfeld[1990] “Engineering Proteins for Purification,” TibTech 8:88-93;Sheibani [1999] “Prokaryotic Gene Fusion Expression Systems and TheirUse in Structural and Functional Studies of Proteins,” Prep. Biochem. &Biotechnol. 29(1):77-90, Marcel Dekker, Inc.; Skerra et al. [1999]“Applications of a Peptide Ligand for Streptavidin: the Strep-tag”,Biomolecular Engineering 16:79-86, Elsevier Science, B. V.; Smith [1998]“Cookbook for Eukaryotic Protein Expression: Yeast, Insect, and PlantExpression Systems,” The Scientist 12(22):20; Smyth et al. [200]“Eukaryotic Expression and Purification of Recombinant ExtracellularMatrix Proteins Carrying the Strep II Tag”, Methods in MolecularBiology, 139:49-57; Unger [1997] “Show Me the Money: ProkaryoticExpression Vectors and Purification Systems,” The Scientist 11(17):20,each of which is hereby incorporated by reference in their entireties),or commercially available tags from vendors such as such as STRATAGENE(La Jolla, Calif.), NOVAGEN (Madison, Wis.), QIAGEN, Inc., (Valencia,Calif.), or InVitrogen (San Diego, Calif.).

Variant polypeptides can, alternatively, have 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61,62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79,80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97,98, or 99 percent identity with the polypeptide sequences of the instantinvention. In a preferred embodiment, a variant or modified polypeptideexhibits approximately 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,95%, 96%, 97%, 98%, or 99% identity to a natural polypeptic of theinvention. Typically, the percent identity is calculated with referenceto the full length, native, and/or naturally occurring polypeptide(e.g., those polypeptides set forth in SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, or 27).

The nomenclature used to describe peptide compounds follows theconventional practice wherein the amino group is presented to the left(the N-terminus) and the carboxyl group to the right (the C-terminus) ofeach amino acid residue. When amino acid residue positions are referredto in an epitope, they are numbered in an amino to carboxyl directionwith position one being the position closest to the amino terminal endof the epitope, or the peptide or protein of which it may be a part. Inthe formulae representing selected specific embodiments of the presentinvention, the amino- and carboxyl-tenninal groups, although notspecifically shown, are in the form they would assume at physiologic pHvalues, unless otherwise specified. In the amino acid structureformulae, each residue is generally represented by standard three-letteror single-letter designations (e.g., as set forth infra). By way ofexample, amino acid substitutions can be carried out without resultingin a substantial modification of the biological activity of thecorresponding modified polypeptides; for example, the replacement ofleucine with valine or isoleucine, of aspartic acid with glutamic acid,of glutamine with asparagine, of arginine with lysine, and the like, thereverse substitutions can be performed without substantial modificationof the biological activity of the polypeptides.

The L-form of an amino acid residue is represented by a capital singleletter or a capital first letter of a three-letter symbol, and theD-form, for those amino acids having D-forms, is represented by a lowercase single letter or a lower case three letter symbol. Glycine has noasymmetric carbon atom and is simply referred to as “Gly” or G. Symbolsfor the amino acids are as follows: (Single Letter Symbol; Three LetterSymbol Amino Acid) A; Ala; Alanine: C; Cys; Cysteine: D; Asp; AsparticAcid: E; Glu; Glutamic Acid: F; Phe; Phenylalanine: G; Gly; Glycine: H;His; Histidine: I; Ile; Isoleucine: K; Lys; Lysine: L; Leu; Leucine: M;Met; Methionine: N; Asn; Asparagine: P; Pro; Proline: Q; Gln; Glutamine:R; Arg; Arginine: S; Ser; Serine: T; Thr; Threonine: V; Val; Valine: W;Trp; Tryptophan: Y; Tyr; Tyrosine.

Amino acid “chemical characteristics” are defined as: Aromatic (F, W,Y); Aliphatic-hydrophobic (L, I, V, M); Small polar (S, T, C); Largepolar (Q, N); Acidic (D, E); Basic (R, H, K); Non-polar: Proline;Alanine; and Glycine.

In order to extend the life of the polypeptides according to theinvention, it may be advantageous to use non-natural amino acids, forexample in the D-form, or alternatively amino acid analogs, for examplesulfur-containing forms of amino acids in the production of “variantpolypeptides”. Alternative means for increasing the life of polypeptidescan also he used in the practice of the instant invention. For example,polypeptides of the invention, and fragments thereof, can berecombinantly modified to include elements that increase the plasma, orserum half-life of the polypeptides of the invention. These elementsinclude, and are not limited to, antibody constant regions (see forexample, U.S. Pat. No. 5,565,335, hereby incorporated by reference inits entirety, including all references cited therein), or other elementssuch as those disclosed in U.S. Pat. Nos. 6,319,691, 6,277,375, or5,643,570, each of which is incorporated by reference in its entirety,including all references cited within each respective patent.Alternatively, the polynucleotides and genes of the instant inventioncan be recombinantly fused to elements, well known to the skilledartisan, that are useful in the preparation of immunogenic constructsfor the purposes of vaccine formulation.

The subject invention also provides biologically active fragments(epitopes) of a polypeptide according to the invention and includesthose peptides capable of eliciting an immune response directed againstP. falciparum, said immune response providing components (B-cells,antibodies, and/or or components of the cellular immune response (e.g.,helper, cytotoxic, and/or suppressor T-cells)) reactive with thebiologically active fragment of a polypeptide; the intact, full length,unmodified polypeptide disclosed herein; or both the biologically activefragment of a polypeptide and the intact, full length, unmodifiedpolypeptides disclosed herein.

Fragments, as described herein, can be obtained by cleaving thepolypeptides of the invention with a proteolytic enzyme (such astrypsin, chymotrypsin, or collagenase) or with a chemical reagent, suchas cyanogen bromide (CNBr). Alternatively, polypeptide fragments can begenerated in a highly acidic environment, for example at pH 2.5. Suchpolypeptide fragments may be equally well prepared by chemical synthesisor using hosts transformed with an expression vector according to theinvention. The transformed host cells contain a nucleic acid, allowingthe expression of these fragments, under the control of appropriateelements for regulation and/or expression of the polypeptide fragments.

In one embodiment, the subject invention provides methods for elicitingan immune response in an individual comprising the administration ofcompositions comprising polypeptides according to the subject inventionto an individual in amounts sufficient to induce an immune response inthe individual. In some embodiments, a “protective” or “therapeuticimmune response” is induced in the individual. A “protective immuneresponse” or “therapeutic immune response” refers to a CTL (or CD8⁺ Tcell) and/or an HTL (or CD4⁺ T cell), and/or an antibody response to anantigen derived from an infectious agent or a tumor antigen, which insome way prevents or at least partially arrests disease symptoms, sideeffects or progression. The protective immune response may also includean antibody response that has been facilitated by the stimulation ofhelper T cells (or CD4⁺ T cells). Additional methods of inducing animmune response in an individual are taught in U.S. Pat. No. 6,419,931,hereby incorporated by reference in its entirety. The term CTL can beused interchangeably with CD8⁺ T-cell(s) and the term HTL can be usedinterchangeably with CD4⁺ T-cell(s) throughout the subject application.

The term “individual” includes mammals which include, and are notlimited to, apes, chimpanzees, orangutans, humans, monkeys ordomesticated animals (pets) such as dogs, cats, guinea pigs, hamsters,Vietnamese pot-bellied pigs, rabbits, ferrets, cows, horses, goats andsheep. In a preferred embodiment, the methods of inducing an immuneresponse contemplated herein are practiced on humans.

Another embodiment of the subject invention provides methods of inducingan immune response in an individual comprising the administration of acomposition comprising polypeptides encoded by the polynucleotides ofthe subject invention in amounts sufficient to induce an immuneresponse. In some embodiments of the invention, the immune responseprovides protective immunity. The composition administered to theindividual may, optionally, contain an adjuvant and may be delivered inany manner known in the art for the delivery of immunogen to a subject.Compositions may also be formulated in any carriers, including forexample, pharmaceutically acceptable carriers such as those described inE. W. Martin's Remington's Pharmaceutical Science, Mack PublishingCompany, Easton, Pa. In a preferred embodiment, compositions may beformulated in incomplete Freund's adjuvant. In various embodiments, thesubject invention provides for diagnostic assays based upon Western blotformats or standard immunoassays known to the skilled artisan. Forexample, antibody-based assays such as enzyme linked immunosorbentassays (ELISAs), radioimmunoassays (RIAs), lateral flow assays,immunochromatographic strip assays, automated flow assays, and assaysutilizing antibody-containing biosensors may be employed for thedetection of the polypeptides, and fragments thereof, provided by thesubject invention. The assays and methods for conducting the assays arewell-known in the art and the methods may test biological samplesqualitatively (presence or absence of polypeptide) or quantitatively(comparison of a sample against a standard curve prepared using apolypeptide of the subject invention) for the presence of one or morepolypeptide of the subject invention. Thus, the subject inventionprovides a method of detecting a P. falciparum polypeptide, or fragmentthereof, comprising contacting a sample with an antibody thatspecifically binds to a polypeptide, or fragment thereof, comprising SEQID NOs: 1-26, or 27 and detecting the presence of an antibody-antigencomplex.

The antibody-based assays can be considered to be of four types: directbinding assays, sandwich assays, competition assays, and displacementassays. In a direct binding assay, either the antibody or antigen islabeled, and there is a means of measuring the number of complexesformed. In a sandwich assay, the formation of a complex of at leastthree components (e.g., antibody-antigen-antibody) is measured. In acompetition assay, labeled antigen and unlabelled antigen compete forbinding to the antibody, and either the bound or the free component ismeasured. In a displacement assay, the labeled antigen is pre-bound tothe antibody, and a change in signal is measured as the unlabelledantigen displaces the bound, labeled antigen from the receptor.

Lateral flow assays can be conducted according to the teachings of U.S.Pat. No. 5,712,170 and the references cited therein. U.S. Pat. No.5,712,170 and the references cited therein are hereby incorporated byreference in their entireties. Displacement assays and flowimmunosensors useful for carrying out displacement assays are describedin: (1) Kusterbeck et al., “Antibody-Based Biosensor for ContinuousMonitoring”, in Biosensor Technology, R. P. Buck et al., eds., MarcelDekker, N.Y. pp. 345-350 (1990); Kusterbeck et al., “A Continuous FlowImmunoassay for Rapid and Sensitive Detection of Small Molecules”,Journal of Immunological Methods, vol. 135, pp. 191-197 (1990); Ligleret al., “Drug Detection Using the Flow Immunosensor”, in BiosensorDesign and Application, J. Findley et al., eds., American ChemicalSociety Press, pp. 73-80 (1992); and Ogert et al., “Detection of CocaineUsing the Flow Immunosensor”, Analytical Letters, vol. 25, pp. 1999-2019(1992), all of which are incorporated herein by reference in theirentireties. Displacement assays and flow immunosensors are alsodescribed in U.S. Pat. No. 5,183,740, which is also incorporated hereinby reference in its entirety. The displacement immunoassay, unlike mostof the competitive immunoassays used to detect small molecules, cangenerate a positive signal with increasing antigen concentration. Oneaspect of the invention allows for the exclusion of Western blots as adiagnostic assay, particularly where the Western blot is a screen ofwhole cell lysates of P. falciparum, or related organisms, againstimmune serum of infected individuals. In another aspect of theinvention, peptide, or polypeptide, based diagnostic assays utilize P.falciparum peptides or polypeptides that have been produce either bychemical peptide synthesis or by recombinant methodologies that utilizenon-plasmodium host cells for the production of peptides orpolypeptides.

Another aspect of the invention provides for the use of peptides,polypeptides, and multi-epitope constructs in assays such as thosetaught in U.S. Pat. No. 5,635,363, which is hereby incorporated byreference in its entirety. Briefly, peptides, polypeptides, andmulti-epitope constructs of the subject invention can be used to formstable multimeric complexes that comprise prepared majorhistocompatibility complex (MHC) protein subunits having a substantiallyhomogeneous bound peptide population. The multimeric MHC-antigen complexforms a stable structure with T cells recognizing the complex throughtheir antigen receptor, thereby allowing for the labeling,identification and separation of specific T cells. The multimericbinding complex has the formula (α-β-P)_(n), where n≧2, usually n≧4, andusually n≧10; α is an α chain of a class I or class II MHC protein. β isa β chain, (the β chain of a class II MHC protein or β₂microglobulin fora MHC class I protein; and P is a peptide antigen. The multimericcomplex stably binds through non-covalent interactions to a T cellreceptor having the appropriate antigenic specificity. The MHC proteinsmay be from any individual. Of particular interest are the human HLAproteins. Included in the HLA proteins are the class II subunitsHLA-DPα, HLA-DPβ, HLA-DQα, HLA-DQβ, HLA-DRα and HLA-DRβ, and the class Iproteins HLA-A, HLA-B, HLA-C, and β₂-microglobulin. In a preferredembodiment, the MHC protein subunits are a soluble foim of the normallymembrane-bound protein. The soluble form is derived from the native formby deletion of the transmembrane domain. Conveniently, the protein istruncated, removing both the cytoplasmic and transmembrane domains. Theprotein may be truncated by proteolytic cleavage, or by expressing agenetically engineered truncated form. For class I proteins, the solubleform will include the α1, α2 and α3 domain. Not more than about 10,usually not more than about 5, preferably none of the amino acids of thetransmembrane domain will be included. The deletion may extend as muchas about 10 amino acids into the α3 domain, preferably none of the aminoacids of the α3 domain will be deleted. The deletion will be such thatit does not interfere with the ability of the α3 domain to fold into adisulfide bonded structure. The class I β chain, β₂-microglobulin, lacksa transmembrane domain in its native form, and need not be truncated.Generally, no Class II subunits will be used in conjunction with Class Isubunits. Soluble class II subunits will include the α1 and α2 domainsfor the α subunit, and the β1 and β2 domains for the β subunit. Not morethan about 10, usually not more than about 5, preferably none of theamino acids of the transmembrane domain will be included. The deletionmay extend as much as about 10 amino acids into the α2 or β2 domain,preferably none of the amino acids of the β2 or β2 domain will bedeleted. The deletion will be such that it does not interfere with theability of the α2 or β2 domain to fold into a disulfide bondedstructure. The monomeric complex (α-β-P) (monomer) is multimerized. Theresulting multimer will be stable over long periods of time. Usually notmore than about 10% of the multimer will be dissociated after storage at4° C. for about one day, more usually after about one week. Preferably,the multimer will be formed by binding the monomers to a multivalententity through specific attachment sites on the α or β subunit, asdescribed below in detail. The multimer may also be formed by chemicalcross-linking of the monomers. A number of reagents capable ofcross-linking proteins are known in the art, illustrative entitiesinclude: azidobenzoyl hydrazide,N-[4-(p-azidosalicylamino)butyl]-3′-[2′-pyridyldithio]propionamide),bis-sulfosuccinimidyl suberate, dimethyladipimidate,disuccinimidyltartrate, N-.gamma.-maleimidobutyryloxysuccinimide ester,N-hydroxy sulfosuccinimidyl-4-azidobenzoate, N-succinimidyl[4-azidophenyl]-1,3′-dithiopropionate, N-succinimidyl[4-iodoacetyl]aminobenzoate, glutaraldehyde, formaldehyde andsuccinimidyl 4-[N-maleimidomethyl]cyclohexane-1 -carboxylate.

The attachment site for binding to a multivalent entity may be naturallyoccurring, or may be introduced through genetic engineering. The sitewill be a specific binding pair member or one that is modified toprovide a specific binding pair member, where the complementary pair hasa multiplicity of specific binding sites. Binding to the complementarybinding member can be a chemical reaction, epitope-receptor binding orhapten-receptor binding where a hapten is linked to the subunit chain.In a preferred embodiment, one of the subunits is fused to an amino acidsequence providing a recognition site for a modifying enzyme. Therecognition sequence will usually be fused proximal to the carboxyterminus of one of the subunit to avoid potential hindrance at theantigenic peptide binding site. Conveniently, an expression cassettewill include the sequence encoding the recognition site.

Modifying enzymes of interest include BirA, various glycosylases,farnesyl protein transferase, protein kinases and the like. The subunitmay be reacted with the modifying enzyme at any convenient time, usuallyafter formation of the monomer. The group introduced by the modifyingenzyme, e.g. biotin, sugar, phosphate, farnesyl, etc. provides acomplementary binding pair member, or a unique site for furthermodification, such as chemical cross-linking, biotinylation, etc. thatwill provide a complementary binding pair member. An alternativestrategy is to introduce an unpaired cysteine residue to the subunit,thereby introducing a unique and chemically reactive site for binding.The attachment site may also be a naturally occurring or introducedepitope, where the multivalent binding partner will be an antibody, e.g.IgG, IgM, etc. Any modification will be at a site, e.g. C-terminalproximal, that will not interfere with binding.

Exemplary of multimer formation is the introduction of the recognitionsequence for the enzyme BirA, which catalyzes biotinylation of theprotein substrate. The monomer with a biotinylated subunit is then boundto a multivalent binding partner, e.g. streptavidin or avidin, to whichbiotin binds with extremely high affinity. Streptavidin has a valency of4, providing a multimer of (α-β-P)₄.

The multivalent binding partner may be free in solution, or may beattached to an insoluble support. Examples of suitable insolublesupports include beads, e.g. magnetic beads, membranes and microtiterplates. These are typically made of glass, plastic (e.g. polystyrene),polysaccharides, nylon or nitrocellulose. Attachment to an insolublesupport is useful when the binding complex is to be used for separationof T cells.

Frequently, the multimeric complex will be labeled, so as to be directlydetectable, or will be used in conjunction with secondary labeledimmunoreagents which will specifically bind the complex. In general thelabel will have a light detectable characteristic. Preferred labels arefluorophors, such as fluorescein isothiocyanate (FITC), rhodamine, TexasRed, phycoerythrin and allophycocyanin. Other labels of interest mayinclude dyes, enzymes, chemiluminescers, particles, radioisotopes, orother directly or indirectly detectable agent. Conveniently, themultivalent binding partner will have the labeling group. Alternatively,a second stage label may be used, e.g. labeled antibody directed to oneof the peptide constituents, and the like.

The binding complex will be used to detect and/or separate antigenspecific T cells. The T cells may be from any source, usually having thesame species of origin as the MHC heterodimer. The T cells may be froman in vitro culture, or a physiologic sample. For the most part, thephysiologic samples employed will be blood or lymph, but samples mayalso involve other sources oft cells, particularly where T cells may beinvasive. Thus other sites of interest are tissues, or associatedfluids, as in the brain, lymph node, neoplasms, spleen, liver, kidney,pancreas, tonsil, thymus, joints, synovia, and the like. The sample maybe used as obtained or may be subject to modification, as in the case ofdilution, concentration, or the like. Prior treatments may involveremoval of cells by various techniques, including centrifugation, usingFicoll-Hypaque, panning, affinity separation, using antibodies specificfor one or more markers present as surface membrane proteins on thesurface of cells, or any other technique that provides enrichment of theset or subset of cells of interest.

The binding complex is added to a suspension comprising T cells ofinterest, and incubated at about 4° C. for a period of time sufficientto bind the available cell surface receptor. The incubation will usuallybe at least about 5 minutes and usually less than about 30 minutes. Itis desirable to have a sufficient concentration of labeling reagent inthe reaction mixture, so that labeling reaction is not limited by lackof labeling reagent. The appropriate concentration is determined bytitration. The medium in which the cells are labeled will be anysuitable medium as known in the art. If live cells are desired a mediumwill be chosen that maintains the viability of the cells. A preferredmedium is phosphate buffered saline containing from 0.1 to 0.5% BSA.Various media are commercially available and may be used according tothe nature of the cells, including Dulbecco's Modified Eagle Medium(dMEM), Hank's Basic Salt Solution (HBSS), Dulbecco's phosphate bufferedsaline (dPBS), RPMI, Iscove's medium, PBS with 5 mM EDTA, etc.,frequently supplemented with fetal calf serum, BSA, HSA, etc.

Where a second stage labeling reagent is used, the cell suspension maybe washed and resuspended in medium as described above prior toincubation with the second stage reagent. Alternatively, the secondstage reagent may be added directly into the reaction mix.

A number of methods for detection and quantitation of labeled cells areknown in the art. Flow cytometry is a convenient means of enumeratingcells that are a small percent of the total population. Fluorescentmicroscopy may also be used. Various immunoassays, e.g. ELISA, RIA, etc.may used to quantitate the number of cells present after binding to aninsoluble support.

Flow cyometry may also be used for the separation of a labeled subset ofT cells from a complex mixture of cells. The cells may be collected inany appropriate medium which maintains the viability of the cells,usually having a cushion of serum at the bottom of the collection tube.Various media are commercially available as described above. The cellsmay then be used as appropriate.

Alternative means of separation utilize the binding complex bounddirectly or indirectly to an insoluble support, e.g. column, microtiterplate, magnetic beads, etc. The cell sample is added to the bindingcomplex. The complex may be bound to the support by any convenientmeans. After incubation, the insoluble support is washed to removenon-bound components. From one to six washes may be employed, withsufficient volume to thoroughly wash non-specifically bound cellspresent in the sample. The desired cells are then eluted from thebinding complex. In particular the use of magnetic particles to separatecell subsets from complex mixtures is described in Miltenyi et al.(1990) Cytometry 11:231-238.

Detecting and/or quantitating specific T cells in a sample or fractionthereof may be accomplished by a variety of specific assays. In general,the assay will measure the binding between a patient sample, usuallyblood derived, generally in the fol in of plasma or serum and thesubject multimeric binding complexes. The patient sample may be useddirectly, or diluted as appropriate, usually about 1:10 and usually notmore than about 1:10,000. Assays may be perfoinied in any physiologicalbuffer, e.g. PBS, normal saline, HBSS, dPBS, etc.

A sandwich assay is perfoli zied by first attaching the multimericbinding complex to an insoluble surface or support. The multimericbinding complex may be bound to the surface by any convenient means,depending upon the nature of the surface, either directly or throughspecific antibodies. The particular manner of binding is not crucial solong as it is compatible with the reagents and overall methods of theinvention. They may be bound to the plates covalently or non-covalently,preferably non-covalently.

The insoluble supports may be any compositions to which the multimericbinding complex can be bound, which is readily separated from solublematerial, and which is otherwise compatible with the overall method ofmeasuring T cells. The surface of such supports may be solid or porousand of any convenient shape. Examples of suitable insoluble supports towhich the receptor is bound include beads, e.g. magnetic beads,membranes and microtiter plates. These are typically made of glass,plastic (e.g. polystyrene), polysaccharides, nylon or nitrocellulose.Microtiter plates are especially convenient because a large number ofassays can be carried out simultaneously, using small amounts ofreagents and samples.

Before adding patient samples or fractions thereof, the non-specificbinding sites on the insoluble support i.e. those not occupied by themultimeric binding complex, are generally blocked. Preferred blockingagents include non-interfering proteins such as bovine serum albumin,casein, gelatin, and the like. Samples, fractions or aliquots thereofare then added to separately assayable supports (for example, separatewells of a microtiter plate) containing support-hound multimeric bindingcomplex.

Generally from about 0.001 to 1 ml of sample, diluted or otherwise, issufficient, usually about 0.01 ml sufficing. Preferably, each sample andstandard will be added to multiple wells so that mean values can beobtained for each. The incubation time should be sufficient for T cellsto bind the insoluble binding complex. Generally, from about 0.1 to 3 hris sufficient, usually 1 hr sufficing.

After incubation, the insoluble support is generally washed of non-boundcomponents. Generally, a dilute physiologic buffer at an appropriate pH,generally 7-8, is used as a wash medium. From one to six washes may beemployed, with sufficient volume to thoroughly wash non-specificallybound T cells present in the sample. After washing, a solutioncontaining specific second receptor is applied. The receptor may be anycompound that binds patient T cells with sufficient specificity suchthat they can be distinguished from other components present. In apreferred embodiment, second receptors are antibodies specific forcommon T cell antigens, either monoclonal or polyclonal sera, e.g.anti-thy-1, anti-CD45, etc.

T cell specific antibodies may be labeled to facilitate direct orindirect quantification of binding. Examples of labels that permitdirect measurement include radiolabels, such as ³H or ¹²⁵I, fluorescers,dyes, beads, chemilumninescers, colloidal particles, and the like.Examples of labels which permit indirect measurement of binding includeenzymes where the substrate may provide for a colored or fluorescentproduct. Examples of suitable enzymes for use in conjugates includehorseradish peroxidase, alkaline phosphatase, malate dehydrogenase andthe like. Where not commercially available, such antibody-enzymeconjugates are readily produced by techniques known to those skilled inthe art.

Alternatively, the second receptor may be unlabeled. In this case, alabeled second receptor-specific compound is employed which hinds to thebound second receptor. Such a second receptor-specific compound can belabelled in any of the above manners. It is possible to select suchcompounds such that multiple compounds bind each molecule of boundsecond receptor. Examples of second receptor/second receptor-specificmolecule pairs include antibody/anti-antibody and avidin (orstreptavidin)/biotin. Since the resultant signal is thus amplified, thistechnique may be advantageous where only a small number oft cells arepresent. An example is the use of a labeled antibody specific to thesecond receptor. More specifically, where the second receptor is arabbit anti-allotypic antibody, an antibody directed against theconstant region of rabbit antibodies provides a suitable second receptorspecific molecule. The anti-immunoglobulin will usually come from anysource other than human, such as ovine, rodentia, particularly mouse, orbovine. The volume, composition and concentration of T cell specificreceptor solution provides for measurable binding to the T cells alreadybound to the insoluble substrate. Generally, the same volume as that ofthe sample is used: from about 0.001 to 1 ml is sufficient, usuallyabout 0.1 ml sufficing. When antibody ligands are used, theconcentration generally will be about 0.1 to 50 μg/ml, preferably about1 μg/ml. The solution containing the second receptor is generallybuffered in the range of about pH 6.5-9.5. The solution may also containan innocuous protein as previously described. The incubation time shouldbe sufficient for the labeled ligand to bind available molecules.Generally, from about 0.1 to 3 hr is sufficient, usually 1 hr sufficing.

After the second receptor or second receptor-conjugate has bound, theinsoluble support is generally again washed free of non-specificallybound second receptor, essentially as described for prior washes. Afternon-specifically bound material has been cleared, the signal produced bythe bound conjugate is detected by conventional means. Where an enzymeconjugate is used, an appropriate enzyme substrate is provided so adetectable product is formed. More specifically, where a peroxidase isthe selected enzyme conjugate, a preferred substrate combination is H₂O₂and O-phenylenediamine which yields a colored product under appropriatereaction conditions. Appropriate substrates for other enzyme conjugatessuch as those disclosed above are known to those skilled in the art.Suitable reaction conditions as well as means for detecting the varioususeful conjugates or their products are also known to those skilled inthe art. For the product of the substrate O-phenylenediamine forexample, light absorbance at 490-495 nm is conveniently measured with aspectrophotometer.

Generally the number of bound T cells detected will be compared tocontrol samples from samples having a different MHC context, e.g. Tcells from an animal that does not express the MHC molecule used to makethe binding complex.

An alternative protocol is to provide anti-T cell reagent, e.g.anti-thy-1, anti-CD45, etc. bound to the insoluble surface. After addingthe sample and washing away non-specifically bound T cells, one or acombination of the subject binding complexes are added, where thebinding complexes are labeled so as not to interfere with the binding toT cells.

It is particularly convenient in a clinical setting to perform theassays in a self-contained apparatus. A number of such methods are knownin the art. The apparatus will generally employ a continuous flow-pathof a suitable filter or membrane, having at least three regions, a fluidtransport region, a sample region, and a measuring region. The sampleregion is prevented from fluid transfer contact with the other portionsof the flow path prior to receiving the sample. After the sample regionreceives the sample, it is brought into fluid transfer relationship withthe other regions, and the fluid transfer region contacted with fluid topermit a reagent solution to pass through the sample region and into themeasuring region. The measuring region may have bound to it themultimeric binding complex, with a conjugate of an enzyme with T cellspecific antibody employed as a reagent, generally added to the samplebefore application. Alternatively, the binding complex may be conjugatedto an enzyme, with T cell specific antibody bound to the measurementregion.

Detection of T cells is of interest in connection with a variety ofconditions associated with T cell activation. Such conditions includeautoimmune diseases, e.g. multiple sclerosis, myasthenia gravis,rheumatoid arthritis, type 1 diabetes, graft vs. host disease, Grave'sdisease, etc.; various forms of cancer, e.g. carcinomas, melanomas,sarcomas, lymphomas and leukemias. Various infectious diseases such asthose caused by viruses, e.g. HIV-1, hepatitis, herpesviruses, entericviruses, respiratory viruses, rhabdovirus, rubeola, poxvirus,paramyxovirus, morbillivirus, etc. are of interest. Infectious agents ofinterest also include bacteria, such as Pneumococcus, Staphylococcus,Bacillus. Streptococcus, Meningococcus, Gonococcus, Eschericia,Klebsiella, Proteus, Pseudomonas, Salmonella, Shigella, Hemophilus,Yersinia, Listeria, Corynebacterium, Vibrio, Clostridia, Chlamydia,Mycobacterium, Helicobacter and Treponema; protozoan pathogens, and thelike. T cell associated allergic responses may also be monitored, e.g.delayed type hypersensitivity or contact hypersensitivity involving Tcells.

Of particular interest are conditions having an association with aspecific peptide or MHC haplotype, where the subject binding complexesmay be used to track the T cell response with respect to the haplotypeand antigen. A large number of associations have been made in diseasestates that suggest that specific MHC haplotypes, or specific proteinantigens are responsible for disease states.

Polypeptide fragments, including immunogenic fragments, for each of SEQID NOs: 1-27 can be any length from at least 5 consecutive amino acidsto 1 amino acid less than a full length polypeptide of any given SEQ IDNO:. Thus, for SEQ ID NO: 1 (used here as a non-limiting example) thepolypeptide fragment can contain any number of consecutive amino acidsfrom 5 to 1903 (for example, 5, 6, 7, . . . , 1901, 1902, 1903). For thesake of brevity, the individual integers between 5 and 1903 have notbeen reproduced herein but are, in fact, specifically contemplated. Inone embodiment, the immunogenic fragments of the invention induceimmunity or protective immunity from disease.

The present invention also provides for the exclusion of any individualfragment (of any given SEQ ID NO:) specified by N-terminal to C-terminalpositions, actual sequence, or of any fragment specified by size (inamino acid residues) as described above. In addition, any number offragments specified by N-terminal and C-terminal positions, actualsequence, or by size (in amino acid residues) as described above may beexcluded as individual species. Further, any number of fragmentsspecified by N-terminal and C-terminal positions or by size (in aminoacid residues) as described above may be combined to provide apolypeptide fragment. These types of fragments may, optionally, includepolypeptide sequences such as linkers, described below.

Where a claim recites “a polypeptide comprising SEQ ID NO: X, orfragments or immunogenic fragments or epitopes of SEQ ID NO:X”, thelanguage “fragments or immunogenic fragments or epitopes of SEQ ID NO:X”specifically excludes identical sub-sequences found within other longernaturally occurring prior art polypeptide or protein sequences that arenot identical to sequence from which the claimed sequence was derived.This does not include instances where such sub-sequences are a part of alarger molecule specifically modified by the hand of man to enhance theimmunogenicity of the fragments of the subject invention. Thus,fragments or immunogenic fragments or epitopes of SEQ ID NO:Xspecifically exclude, and are not to be considered anticipated, wherethe fragment is a sub-sequence of another naturally occurringnon-malarial peptide, polypeptide, or protein isolated from a bacterial,viral, reptilian, insect, avian, or mammalian source and is identifiedin a search of protein sequence databases.

Fragments or immunogenic fragments or epitopes of the invention mayfurther contain linkers that facilitate the attachment of the fragmentsto a carrier molecule for the stimulation of an immune response ordiagnostic purposes. The linkers can also be used to attach fragmentsaccording to the invention to solid support matrices for use in affinitypurification protocols. In this aspect of the invention, the linkersspecifically exclude, and are not to be considered anticipated, wherethe fragment is a subsequence of another peptide, polypeptide, orprotein as identified in a search of protein sequence databases asindicated in the preceding paragraph. In other words, the non-identicalportions of the other peptide, polypeptide, of protein are notconsidered to be a “linker” in this aspect of the invention.Non-limiting examples of “linkers” suitable for the practice of theinvention include chemical linkers (such as those sold by Pierce,Rockford, Ill.) and peptides that allow for the connection of theimmunogenic fragment to a carrier molecule (see, for example, linkersdisclosed in U.S. Pat. Nos. 6,121,424, 5,843,464, 5,750,352, and5,990,275, hereby incorporated by reference in their entirety). Invarious embodiments, the linkers can be up to 50 amino acids in length,up to 40 amino acids in length, up to 30 amino acids in length, up to 20amino acids in length, up to 10 amino acids in length, or up to 5 aminoacids in length. Of course, the linker may be any pre-selected number ofamino acids (up to 50 amino acids) in length.

In various embodiments, polypeptides suitable for use in variousdisclosed methods of the subject invention can be selected from thegroup consisting of: a) a polypeptide comprising a polypeptide sequenceselected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16 ,17, 18, 19, 20, 21 ,22, 23, 24, 25,26, and 27; b) a variant polypeptide having at least about 20% to 99.99%identity to a polypeptide selected from the group consisting of SEQ IDNO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 ,17, 18, 19,20, 21, 22, 23, 24, 25, 26, and 27; c) a fragment of a polypeptide or avariant polypeptide of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27, whereinsaid fragment or variant has substantially the same serologic reactivityor substantially the same T-cell reactivity as the native polypeptide;d) a multi-epitope construct; and e) combinations thereof.

Multi-Epitope Constructs

As indicated supra, the subject invention provides for “multi-epitopeconstructs”. A “multi-epitope construct” comprises: 1) nucleic acidsthat encode multiple polypeptide epitopes (of any length) that can bindto one or more molecules functioning in the immune system; or 2)polypeptides comprising multiple polypeptide epitopes that can bind toone or more molecules functioning in the immune system. “Multi-epitopeconstructs” can, optionally, contain “flanking” or “spacing” residuesbetween each epitope. Some embodiments provide for “multi-epitopeconstructs” that comprise a series of the same epitope (termed“homopolymers”). Other embodiments provide for “multi-epitopeconstructs” that comprise a combination or series of different epitopes,optionally connected by “flanking” or “spacing” residues (termed“heteropolymers”). In some embodiments, “multi-epitope constructs” mayexclude full-length polypeptides from which the epitopes are obtained(e.g., the polypeptides of SEQ ID NOs: 1-27). In certain preferredembodiments, the epitopes used in the formation of the multi-epitopeconstruct are selected from those set forth in Table 2, Table 3, Table4, Table 5, and/or Table 6 and any epitope set forth in these Tables 2-6can be mixed and/or matched any other epitope set forth in any of theaforementioned Tables 2-6.

Multi-epitope constructs may be of “high affinity” or “intermediateaffinity”. As used herein, “high affinity” with respect to HLA class Imolecules is defined as binding with an IC₅₀, or KD value, of 50 nM orless; “intermediate affinity” with respect to HLA class I molecules isdefined as binding with an IC₅₀ or KD value of between about 50 andabout 500 nM. “High affinity” with respect to binding to HLA class IImolecules is defined as binding with an IC₅₀ or KD value of 100 nM orless; “intermediate affinity” with respect to binding to HLA class IImolecules is defined as binding with an IC₅₀ or KD value of betweenabout 100 and about 1000 nM.

The multi-epitope constructs described herein preferably include five ormore, ten or more, fifteen or more, twenty or more, or twenty-five ormore epitopes. Other embodiments provide multi-epitope constructs thatcomprise at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37,38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55,56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73,74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91,92, 93, 94, 95, 96, 97, 98, or 99 epitopes. All of the epitopes in amulti-epitope construct may be from one organism (e.g., the epitopes areobtained from P. falciparum), or the multi-epitope construct may includeepitopes present in two or more different organisms (e.g., some epitopesfrom P. falciparum and some epitopes from another organism).Additionally, the same epitope may be present in a multi-epitopeconstruct at more than one location in the construct. In someembodiments, novel epitopes of the subject invention may be linked toknown epitopes of an organism (e.g., P. falciparum or another organism).

A “multi-epitope vaccine,” is a vaccine comprising multiple epitopes. Amulti-epitope vaccine can induce an immune response and is administeredto an individual in an amount sufficient to induce an immune response inthe individual. In sonic embodiments, the immune response induced by themulti-epitope vaccine is a protective immune response against a givenorganism, pathogen, or pathologic condition (e.g., P. falciparum).

In certain embodiments, the epitopes of a multi-epitope construct or thepolypeptides disclosed herein interact with an antigen binding site ofan antibody molecule, a class I HLA, a T-cell receptor, and/or a classII HLA molecule. In certain preferred embodiments, the epitopes interactwith an FILA molecule (e.g., class I or class II) or a T-cell receptor.In an even more preferred embodiment, the epitope interacts with both anHLA molecule (e.g., class I or class II) and a T-cell receptor. Invarious embodiments, all of the nucleic acids in a multi-epitopeconstruct can encode class I HLA epitopes or class II HLA epitopes.Multi-epitope constructs comprising epitopes that interact exclusivelywith class I HLA molecules may be referred to as “CTL multi-epitopeconstructs” (or “CD8⁺ T cell multi-epitope constructs”). Multi-epitopeconstructs comprising epitopes that interact exclusively with class IIHLA molecules may be referred to as “HTL multi-epitope constructs” (or“CD4⁺ T cell multi epitope constructs”). Some multi-epitope constructs(designated “TL multi-epitope constructs”) can have a subset of themulti-epitope nucleic acids encoding class I HLA epitopes and anothersubset of the multi-epitope nucleic acids encoding class II HLA epitopes(e.g., the constructs stimulate both CTL (i.e., CD8⁺ T cell) and HTL(i.e., CD4⁺ T cell) of the immune system). Other multi-epitopeconstructs can provide epitopes that interact exclusively with B-cellsor immunoglobulin molecules and are designated “BL multi-epitopeconstructs”. Multi-epitope constructs that provide epitopes thatinteract with B-cells (and/or immunoglobulin molecules) and furtherprovide class I HLA epitopes and class II HLA epitopes are designated“immune system (IMS) multi-epitope constructs”. In certain embodiments,multi-epitope constructs can provide class I or class II epitopes (e.g.,CTL (i.e., CD8⁺ T cell) epitopes or HTL (i.e., CD4⁺ T cell) epitopes)and BL epitopes. “Human Leukocyte Antigen” or “HLA” is a human class Ior class II Major Histocompatibility Complex (MHC) protein (see, e.g.,Stites, et al., IMMUNOLOGY, 8^(TH) ED., Lange Publishing, Los Altos,Calif. (1994)).

CTL epitope (class I epitope) (i.e., CD8⁺ T cell epitope) encodingnucleic acids preferably provide an epitope peptide of about eight toabout thirteen amino acids in length (e.g., 8, 9, 10, 11, 12 or 13),more preferably about eight to about eleven amino acids in length, andmost preferably about nine amino acids in length. HTL (CD4⁺ T-cell)epitope nucleic acids can provide an epitope peptide of about seven toabout twenty three (e.g., 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,19, 20, 21, 22 or 23) preferably about seven to about seventeen (e.g.,7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or 17, more preferably about elevento about fifteen (e.g., 11, 12, 13, 14 or 15), and most preferably aboutthirteen amino acids in length.

“Degenerate binding” indicates that a peptide is bound by more than oneHLA molecule; a synonym is “cross reactive binding.” “Cross reactivebinding” may also be used to define the interaction of an antigen withmultiple populations of antibodies. In certain preferred embodiments,epitopes disclosed herein do not exhibit cross reactive or degeneratebinding. Other embodiments encompass degenerate or cross reactivebinding of antigens or epitopes.

With regard to a particular amino acid sequence, an “epitope” is a setof amino acid residues that is involved in recognition by a particularimmunoglobulin, or in the context of T cells, those residues necessaryfor recognition by T cell receptor proteins and/or MajorHistocompatibility Complex (MHC) receptors. In an immune system setting,in vitro or in vivo, an epitope is the collective features of amolecule, such as primary, secondary and tertiary peptide structure, andcharge, that together form a site recognized by an immunoglobulin, Tcell receptor or HLA molecule. Throughout this disclosure epitope andpeptide are often used interchangeably. It is to be appreciated,however, that isolated or purified protein or peptide molecules largerthan and comprising an epitope of the invention are still within thebounds of the invention.

A “flanking” or “linking” residue is a residue that is positioned nextto an epitope. A flanking residue can be introduced or inserted at aposition adjacent to the N-terminus or the C-terminus of an epitope.Flanking residues suitable for use in the subject invention aredisclosed, for example, in U.S. Pat. No. 6,419,931, which is herebyincorporated by reference in its entirety, including all sequences,figures, references, and tables.

An “immunogenic peptide” or “peptide epitope” is a peptide thatcomprises an allele-specific motif or supermotif such that the peptidewill bind an HLA molecule and induce a CTL (or CD8⁺ T cell) and/or HTL(or CD4⁺ T cell) response. An “immunogenic peptide” or “peptide epitope”can also be a peptide that comprises a motif that binds to antibodymolecules or B-cells found in the immune system of an individual. Thus,immunogenic peptides of the invention are capable of binding to anantibody molecule, a B-cell, or appropriate HLA molecule and thereafterinducing an immune response (e.g., the induction of antibody production,a cytotoxic T cell response, or a helper T cell response) to the antigenfrom which the immunogenic peptide is derived.

The term “residue” refers to an amino acid or amino acid mimeticincorporated into a peptide or protein by an amide bond or amide bondmimetic.

A “spacer” or “linker” refers to a sequence that is inserted between twoepitopes in a multi-epitope construct to prevent the occurrence ofjunctional epitopes and/or to increase the efficiency of processing. Amulti-epitope construct may have one or more spacer nucleic acids. Aspacer nucleic acid may flank each epitope nucleic acid in a construct,or the spacer nucleic acid to epitope nucleic acid ratio may be about 2to 10, about 5 to 10, about 6 to 10, about 7 to 10, about 8 to 10, orabout 9 to 10, where a ratio of about 8 to 10 has been determined toyield favorable results for some constructs. The spacer nucleic acid mayencode one or more amino acids. A spacer nucleic acid flanking a class IHLA epitope in a multi-epitope construct is preferably between one andabout eight amino acids in length. A spacer nucleic acid flanking aclass II HLA epitope in a multi-epitope construct is preferably greaterthan five, six, seven, or more amino acids in length, and morepreferably five or six amino acids in length. The number of spacers in aconstruct, the number of amino acids in a spacer, and the amino acidcomposition of a spacer can be selected to optimize epitope processingand/or minimize junctional epitopes. It is preferred that spacers areselected by concomitantly optimizing epitope processing and junctionalmotifs. Suitable amino acids for optimizing epitope processing aredescribed herein. Also, suitable amino acid spacing for minimizing thenumber of junctional epitopes in a construct are described herein forclass I and class II HLAs. For example, spacers flanking class II HLAepitopes preferably include G, P, and/or N residues as these are notgenerally known to be primary anchor residues (see, e.g.,PCT/US00/19774). A particularly preferred spacer for flanking a class IIHLA epitope includes alternating G and P residues, for example,(GP)_(n), (PG)_(n), (GP)_(n)G, or (PG)_(n)P, and so forth, where n is aninteger between one and ten, preferably two or about two, and where aspecific example of such a spacer is GPGPG.

In some multi-epitope constructs, it is sufficient that each spacernucleic acid encodes the same amino acid sequence. In multi-epitopeconstructs having two spacer nucleic acids encoding the same amino acidsequence, the spacer nucleic acids encoding those spacers may have thesame or different nucleotide sequences, where different nucleotidesequences may be preferred to decrease the likelihood of unintendedrecombination events when the multi-epitope construct is inserted intocells.

In other multi-epitope constructs, one or more of the spacer nucleicacids may encode different amino acid sequences. While many of thespacer nucleic acids may encode the same amino acid sequence in amulti-epitope construct, one, two, three, four, five or more spacernucleic acids may encode different amino acid sequences, and it ispossible that all of the spacer nucleic acids in a multi-epitopeconstruct encode different amino acid sequences. Spacer nucleic acidsmay be optimized with respect to the epitope nucleic acids they flank bydetermining whether a spacer sequence will maximize epitope processingand/or minimize junctional epitopes, as described herein.

Multi-epitope constructs may be distinguished from one another accordingto whether the spacers in one construct optimize epitope processing orminimize junctional epitopes over another construct, and preferably,constructs may be distinguished where one construct is concomitantlyoptimized for epitope processing and junctional epitopes over the other.Computer assisted methods and in vitro and in vivo laboratory methodsfor determining whether a construct is optimized for epitope processingand junctional motifs are described herein.

“Multi-epitope constructs of the invention may also be “optimized”. Theterm “optimized” or “optimizing” refers to increasing the immunogenicityor antigenicity of a multi-epitope construct having at least one epitopepair by sorting epitopes to minimize the occurrence of junctionalepitopes, inserting flanking residues that flank the C-terminus orN-terminus of an epitope, and inserting spacer residue to furtherprevent the occurrence of junctional epitopes or to provide a flankingresidue. An increase in immunogenicity or antigenicity of an optimizedmulti-epitope construct is measured relative to a multi-epitopeconstruct that has not been constructed based on the optimizationparameters and is using assays known to those of skill in the art, e.g.,assessment of immunogenicity in HLA transgenic mice, ELISPOT,interferon-gamma release assays, tetramer staining, chromium releaseassays, and presentation on dendritic cells.

The subject invention also concerns antibodies that bind to polypeptidesof the invention. Antibodies that are immunospecific for the malarialpolypeptides set forth herein are specifically contemplated. In variousembodiments, antibodies which do not cross react with other proteins ormalarial proteins are also specifically contemplated. The antibodies ofthe subject invention can be prepared using standard materials andmethods known in the art (see, for example, Monoclonal Antibodies:Principles and Practice, 1983; Monoclonal Hybridoma Antibodies:Techniques and Applications, 1982; Selected Methods in CellularImmunology, 1980; Immunological Methods, Vol. II, 1981; PracticalImmunology, and Kohler et al. [1975] Nature 256:495).

The term “antibody” is used in the broadest sense and specificallycovers monoclonal antibodies (including full length monoclonalantibodies), polyclonal antibodies, multispecific antibodies (e.g.,bispecific antibodies), and antibody fragments so long as they exhibitthe desired biological activity, particularly neutralizing activity.“Antibody fragments” comprise a portion of a full length antibody,generally the antigen binding or variable region thereof. Examples ofantibody fragments include Fab, Fab′, F(ab′)₂, and Fv fragments;diabodies; linear antibodies; single-chain antibody molecules; andmulti-specific antibodies formed from antibody fragments.

The term “monoclonal antibody” as used herein refers to an antibodyobtained from a population of substantially homogeneous antibodies,i.e., the individual antibodies comprising the population are identicalexcept for possible naturally occurring mutations that may be present inminor amounts. Monoclonal antibodies are highly specific, being directedagainst a single antigenic site. Furthermore, in contrast toconventional (polyclonal) antibody preparations that typically includedifferent antibodies directed against different determinants (epitopes),each monoclonal antibody is directed against a single determinant on theantigen. The modifier “monoclonal” indicates the character of theantibody as being obtained from a substantially homogeneous populationof antibodies, and is not to be construed as requiring production of theantibody by any particular method. For example, the monoclonalantibodies to be used in accordance with the present invention may bemade by the hybridoma method first described by Kohler et al. [1975]Nature 256: 495, or may be made by recombinant DNA methods (see, e.g.,U.S. Pat. No. 4,816,567). The “monoclonal antibodies” may also beisolated from phage antibody libraries using the techniques described inClackson et al. [1991] Nature 352: 624-628 and Marks et al. [1991]J.Mol. Biol. 222: 581-597, for example.

The monoclonal antibodies described herein specifically include“chimeric” antibodies (immunoglobulins) in which a portion of the heavyand/or light chain is identical with or homologous to correspondingsequences in antibodies derived from a particular species or belongingto a particular antibody class or subclass, while the remainder of thechain(s) is identical with or homologous to corresponding sequences inantibodies derived from another species or belonging to another antibodyclass or subclass, as well as fragments of such antibodies, so long asthey exhibit the desired biological activity (U.S. Pat. No. 4,816,567;and Morrison et al. [1984] Proc. Natl. Acad Sci. USA 81: 6851-6855).Also included are humanized antibodies, such as those taught in U.S.Pat. Nos. 6,407,213 or 6,417,337 which are hereby incorporated byreference in their entirety.

“Single-chain Fv” or “sFv” antibody fragments comprise the V_(H) andV_(L) domains of an antibody, wherein these domains are present in asingle polypeptide chain. Generally, the Fv polypeptide furthercomprises a polypeptide linker between the V_(H) and V_(L) domains whichenables the sFv to form the desired structure for antigen binding. For areview of sFv see Pluckthun in The Pharmacology of Monoclonal Antibodies[1994] Vol. 113:269-315, Rosenburg and Moore eds. Springer-Verlag, NewYork.

The term “diabodies” refers to small antibody fragments with twoantigen-binding sites, which fragments comprise a heavy chain variabledomain (V_(H)) connected to a light chain variable domain (V_(L)) in thesame polypeptide chain (V_(H)-V_(L)). Diabodies are described more fullyin, for example, EP 404,097; WO 93/11161; and Hollinger et al. [1993]Proc. Natl. Acad. Sci. USA 90: 6444-6448. The term “linear antibodies”refers to the antibodies described in Zapata et al. [1995] Protein Eng.8(10):1057-1062.

An “isolated” antibody is one which has been identified and separatedand/or recovered from a component of its natural environment.Contaminant components of its natural environment are materials whichwould interfere with diagnostic or therapeutic uses for the antibody,and may include enzymes, hormones, and other proteinaceous ornonproteinaceous solutes. In preferred embodiments, the antibody will bepurified (1) to greater than 95% by weight of antibody as determined bythe Lowry method, and most preferably more than 99% by weight, (2) to adegree sufficient to obtain at least 15 residues of N-terminal orinternal amino acid sequence by use of a spinning cup sequenator, or (3)to homogeneity by SDS-PAGE under reducing or nonreducing conditionsusing Coomassie blue or, preferably, silver stain. Isolated antibodyincludes the antibody in situ within recombinant cells since at leastone component of the antibody's natural environment will not be present.Ordinarily, however, isolated antibody will be prepared by at least onepurification step.

The terms “comprising”, “consisting of” and “consisting essentially of”are defined according to their standard meaning. The terms may besubstituted for one another throughout the instant application in orderto attach the specific meaning associated with each term. The phrases“isolated” or “biologically pure” refer to material that issubstantially or essentially free from components which normallyaccompany the material as it is found in its native state. Thus,isolated peptides in accordance with the invention preferably do notcontain materials normally associated with the peptides in their in situenvironment. “Link” or “join” refers to any method known in the art forfunctionally connecting peptides, including, without limitation,recombinant fusion, covalent bonding, disulfide bonding, ionic bonding,hydrogen bonding, and electrostatic bonding.

Following are examples which illustrate procedures for practicing theinvention. These examples should not be construed as limiting. Allpercentages are by weight and all solvent mixture proportions are byvolume unless otherwise noted.

In this disclosure, “binding data” results are often expressed in termsof “IC₅₀'s.” IC₅₀ is the concentration of peptide in a binding assay atwhich 50% inhibition of binding of a reference peptide is observed.Given the conditions in which the assays are run (i.e., limiting HLAproteins and labeled peptide concentrations), these values approximateKD values. Assays for deteimining binding are described in detail, e.g.,in PCT publications WO 94/20127 and WO 94/03205 (each of which is herebyincorporated by reference in its entirety). It should be noted that IC₅₀values can change, often dramatically, if the assay conditions arevaried, and depending on the particular reagents used (e.g., HLApreparation, etc.). For example, excessive concentrations of HLAmolecules will increase the apparent measured IC₅₀ of a given ligand.Alternatively, binding is expressed relative to a reference peptide.Although as a particular assay becomes more, or less, sensitive, theIC₅₀'s of the peptides tested may change somewhat, the binding relativeto the reference peptide will not significantly change. For example, inan assay run under conditions such that the IC₅₀ of the referencepeptide increases 10-fold, the IC₅₀ values of the test peptides willalso shift approximately 10-fold. Therefore, to avoid ambiguities, theassessment of whether a peptide is a good, intermediate, weak, ornegative binder is generally based on its IC₅₀, relative to the IC₅₀ ofa standard peptide. Binding may also be determined using other assaysystems including those using: live cells (e.g., Ceppellini et al.,Nature 339:392, 1989; Christnick et al., Nature 352:67, 1991; Busch etal., Int. Immunol. 2:443, 19990; Hill et al., J. Immunol. 147:189,1991;del Guercio et al., J. Immunol. 154:685, 1995), cell free systems usingdetergent lysates (e.g., Cerundolo et al., J Immunol. 21:2069, 1991),immobilized purified MHC (e.g., Hill et al., J. Immunol. 152, 2890,1994; Marshall et al., J Immunol. 152:4946, 1994), ELISA systems (e.g.,Reay et al., EMBO J. 11:2829, 1992), surface plasmon resonance (e.g.,Khilko et al., J. Biol. Chem. 268:15425, 1993); high flux soluble phaseassays (Hammer et al., J. Exp. Med. 180:2353, 1994), and measurement ofclass I MHC stabilization or assembly (e.g., Ljunggren et al., Nature346:476, 1990; Schumacher et al, Cell 62:563, 1990; Townsend et al.,Cell 62:285, 1990; Parker et al., J. lmmunol. 149:1896, 1992). PredictedIC₅₀ values may be referred to as PIC values and measured IC₅₀ valuesmay be referred to a MIC values.

EXAMPLE 1

Starting with 27 open reading frames defined by Multidimensional ProteinIdentification Technology, 9 highly antigenic proteins were identified.These highly antigenic proteins were recognized by volunteers immunizedwith irradiated sporozoites; mock immunized individuals (controls)failed to recognize these proteins. Several of these nine proteins weremore antigenic than previously well-characterized proteins.

To identify and prioritize a set of ORFs representing antigenspotentially expressed in the sporozoite and intrahepatic stage of theparasite life cycle, MS/MS spectra of peptide sequences generated byMultidimensional Protein Identification Technology (MudPIT) (Washburn,M. P., Wolters, D., & Yates, J. R. 3^(rd). Large-scale analysis of theyeast proteome by multidimensional protein identification technology.Nat. Biotechnol. 19, 242-247 (2001)) of P. falciparum sporozoitepreparations were scanned against the P. falciparum genomic sequencedatabase using SEQUEST™ software (Florens, L. et al. A proteomic view ofthe Plasmodium falciparum life cycle. Submitted). A panel of 27 ORF's(10 expressed only in sporozoites, and 17 common to other stages of theparasite life cycle) were selected. Their size ranged between 96-4544amino acids (mean 1252), the percentage of the protein covered byidentified peptides ranged between 0.5-49.5%, and the frequency ofrecognition in the P. falciparum proteome dataset ranged between 16peptide hits from 6 different sporozoite runs (antigen 2) to singlepeptide hits (antigens 1, 11, 14, 16, 19 and 25. When searched againstthe final P. falciparum database using refined gene model predictions,and taking into consideration genomic sequence information from theAnopheles (vector) and human (host) databases, 19 of the 27 antigenscould be identified using stringent selection criteria and six otherscould be identified only with relaxed criteria.

Amino acid sequences from the 27 ORFs were scanned with HLA-A1, A2,A3/A11, A24 and DR supertype PIC algorithms; a total of 3241 peptideswere identified (range=14-435; mean=120 sequences per antigen). A set of1142 sequences was synthesized (range=13-50; mean=42), selecting the top10 scorers per supertype per antigen for larger ORFs. Control sets ofpeptides were synthesized from 4 known antigens (PfCSP, PfSSP2, PfLSA1and PfEXP1). Next, predicted epitopes were tested for their capacity toinduce recall IFN-γ immune responses using PBMC from volunteersimmunized with irradiated P. falciparum sporozoites and either protected(n=4) or not protected (n=4) against challenge with infectioussporozoites, or control volunteers mock immunized in parallel (n=4) (seeTable 1). Peptides were tested as pools, at 1 μg/ml each peptide witheach antigen represented by a separate pool, by IFN-γ ELIspot (Washburn,M. P., Wolters, D., & Yates, J. R. 3^(rd). Large-scale analysis of theyeast proteome by multidimensional protein identification technology.Nat. Biotechnol. 19, 242-247 (2001)). Positive and negative controlepitopes from well characterized antigens (CMV, Influenza, EBV, HIV)were also included.

Considering a stimulation index (ratio test response/control) >2.0 aspositive, 19 of the 27 unknown antigens were recognized by at least 1 of8 irradiated sporozoite immunized volunteers, but not by any of the 4mock immunized controls (Table 1). Nine of the 27 antigens (#2, 5, 3,18, 22, 21, 13, 11, 20) were recognized by at least 50% of irradiatedsporozoite volunteers in at least 25% of assays, 3 antigens (#1, 12, 17)were recognized by at least 25% of volunteers in at least 15% of assays,and 7 antigens (#6, 7, 9, 14, 15, 16, 19) were recognized by at least10% volunteers in at least 5% of assays. Eight of the 27 unknownantigens (#4, 8, 10, 23, 24, 25, 26, 27) failed to induce IFN-γresponses of sufficient magnitude to meet our criteria of positivity.Pools of predicted epitopes from the known antigens, PfCSP, PfSSP2,PfLSA1 and PfEXP1, were also recognized by irradiated sporozoitevolunteers although the frequency of response to those pools wassomewhat lower than that to pools of peptides representing previouslyvalidated epitopes derived from the same antigens (Doolan, D. L. et al.Degenerate cytotoxic T cell epitopes from P. falciparum restricted bymultiple HLA-A and HLA-B supertype alleles. Immunity. 7, 97-112 (1997);Doolan, D. L. et al. HLA-DR-promiscuous T cell epitopes from Plasmodiumflaciparum pre-erthrocytic-stage antigens restricted by multiple HLAclass II alleles. J Immunol. 165:1123-1137 (2000); Wang, R., et al.Induction of CD4(+) T cell-dependent CD8(+) type 1 responses in humansby a malaria DNA vaccine. Proc. Natl. Acad. Sci. U.S.A. 98, 10817-10822(2001)) (Table 1). Particularly noteworthy, the reactivity againstseveral of the newly identified antigens greatly exceeded thereactivities observed against all 4 known antigens For example, bothantigens 2 and 5 were recognized by 7/8 irradiated sporozoite volunteersin 9/16 assays, and antigens 3 and 18 were recognized by 6/8 irradiatedsporozoite volunteers in 6/16 assays.

Results show that HLA-A2 peptide pools from antigens 2, 5 and 13, andHLA-A1 and HLA-DR peptide pools from antigens 2 and 5, are recognized byirradiated sporozoite volunteers who express the respective HLA alleles,but not by mock immunized controls. Deconvolution at the level ofindividual epitopes is in progress. Additionally, a comprehensiveanalysis of HLA binding against the A1, A2, A3/11, A24, and DR1supertypes has been completed for selected antigens. Several degeneratebinders have been identified for each supertype/antigen combination, and50 to 70% of the predicted peptides have been identified as degenerateHLA binders.Further analysis also revealed that the antigenicity resultscorrelate to a large degree with the proteomic data. For example, of 9antigens associated with high immune reactivity, 7 were identified bymultiple peptide hits in multiple MudPIT runs

All patents, patent applications, provisional applications,polynucleotide sequences, amino acid sequences, tables and publicationsreferred to or cited herein are incorporated by reference in theirentirety, including all figures, to the extent they are not inconsistentwith the explicit teachings of this specification. It should beunderstood that the examples and embodiments described herein are forillustrative purposes only and that various modifications or changes inlight thereof will be suggested to persons skilled in the art and are tobe included within the spirit and purview of this application.

TABLE 1 Summary of immune reactivities against the panel of 27 putativeantigens and 4 known antigens. MOCK IRRADIATED SPOROZOITE IMMUNIZEDIMMUNIZED # vol % vol # % SI SFC # vol # Antigen respond respond assaysassays respond respond respond assays 1 3 37.5 3 18.75 2.5 59.3 0 0 2 8100 9 56.25 2.9 110.4 0 0 3 6 75 6 37.5 2.6 119.1 0 0 4 0 — — — — — 0 05 7 87.5 9 56.25 2.8 101.8 0 0 6 1 12.5 1 6.25 2.4 88.3 0 0 7 1 12.5 16.25 2.1 43.3 0 0 8 0 — — — — — 0 0 9 2 25 2 12.5 2.5 32.0 0 0 10 0 — —— — — 0 0 11 4 50 4 25 3.1 81.3 0 0 12 3 37.5 3 18.75 2.2 48.2 0 0 13 450 5 31.25 2.9 92.2 0 0 14 1 12.5 1 6.25 2.2 55.3 0 0 15 2 25 2 12.5 2.528.8 0 0 16 2 25 2 12.5 2.2 27.2 0 0 17 3 37.5 3 18.75 2.4 57.6 0 0 18 675 6 37.5 2.2 58.4 0 0 19 2 25 2 12.5 2.7 31.3 0 0 20 4 50 4 25 2.5 74.80 0 21 4 50 5 31.25 2.3 48.2 0 0 22 5 62.5 5 31.25 2.9 108.4 0 0 23 0 —— — — — 0 0 24 0 — — — — — 0 0 25 0 — — — — — 0 0 26 0 — — — — — 0 0 270 — — — — — 0 0 TOTAL UNKNOWNS 1-8 44.7 3.8 24.0 2.5 66.6 “HIGH” 4-866.7 5.9 36.8 2.7 88.3 “INTERMEDIATE” 3 37.5 3.0 18.8 2.4 55.0 “LOW” 1-219.6 1.6 9.8 2.4 43.8 Range 1-8 12.5-100  1-9 6.25-56.25 2.1-3.127.2-110.4 KNOWNS (@1 ug/ml) predicted 1.4 17.2 1.4 8.6 2.9 57.3 Range1-3 12.5-37.5 1-3 6.25-18.75 2.0-3.4 30.5-137.4 KNOWNS (@1 ug/ml)validated 4.0 50.0 3.8 23.4 3.5 64.0 Range 3-5 37.5-62.5 3-6 18.75-37.5 3.5-3.6 46.6-91.4  TOTAL KNOWNS (@1 ug/ml) 2.3 28.1 2.2 13.5 3.2 60.0Range 1-5 12.5-62.5 1-6 6.25-37.5  2.0-3.6 30.5-137.4 TOTAL KNOWNS (@10ug/ml) 4-8 81.3 7.8 60.9 11.1  588.2 CMV/EBV/Flu 7 87.5 12.0 50.0 4.059.0 4 100

TABLE 2 Pf-derived A1 supertype peptides with PIC <20 nM Addn MalariaSource Accession Peptide locus info No. Position No. Sequence 331.t00003Chromosome10 216 98.0038 KTNKWEDIY 331.t00003 Chromosome10 790 98.0039KSIYIFYTY 331.t00003 Chromosome10 986 98.0040 GTFTFQNMY 331.t00003Chromosome10 1298 98.0041 CNDGNILYY 331.t00003 Chromosome10 1379 98.0042YFECIMKLY 331.t00003 Chromosome10 1389 98.0043 VYEGKLKKY 331.t00003Chromosome10 1650 98.0001 VVDLFCGVGY 331.t00003 Chromosome10 177098.0044 FSSINTYDY 331.t00003 Chromosome10 1803 98.0045 VSNVEDSNY331.t00003 Chromosome10 1831 98.0046 NSNYNKKLY 18.000811 Chr12Contig18182 98.0047 KVSDEIWNY MY924Fe3.p1t1 92 98.0048 ISGEGLIIY MY924Fe3.p1t1215 98.0002 FVEDSSSFLY MY924Fe3.p1t1 384 98.0049 DSDSSNVLY MY924Fe3.p1t1561 98.0050 SQDVFIIEY MY924Fe3.p1t1 1028 98.0051 NSMFHIIMY MY924Fe3.p1t11093 98.0052 SSYNLFEEY MY924Fe3.p1t1 1258 98.0053 SSGKTFICYMY924Fe3.p1t1 1340 98.0054 ILENILLSY MY924Fe3.p1t1 1439 98.0055FSDLILYVY MY924Fe3.p1t1 2318 98.0056 HIENILLKY MP03001 MAL3P2.11CAB38998 14 98.0057 FVEALFQEY MP03001 MAL3P2.11 CAB38998 310 98.0058PSDKHIKEY 1369.t00001 Chromosome 11 38 98.0059 IMNHLMTLY 1369.t00001Chromosome 11 149 98.0060 LIENELMNY 1369.t00001 Chromosome 11 18298.0061 NVDQQNDMY 1369.t00001 Chromosome 11 309 98.0062 SSFFMNRFY1369.t00001 Chromosome 11 342 98.0063 NHEQKLSEY 1369.t00001Chromosome 11 347 98.0003 LSEYYDXDIY 1369.t00001 Chromosome 11 36398.0064 QEEQKKYIY 699.t00001 Chromosome I1 313 98.0065 DSQNELTNY699.t00001 Chromosome 11 441 98.0004 FSFFFSLIDY 699.t00001 Chromosome 11480 98.0066 CHEMKAEFY 699.t00001 Chromosome 11 548 98.0067 MFSSIFENY699.t00001 Chromosome 11 749 98.0068 NSLILLNLY 699.t00001 Chromosome 11859 98.0069 YIDNDINIY 699.t00001 Chromosome 11 919 98.0070 EEDKTYELY699.t00001 Chromosome 11 922 98.0071 KTYELYQKY 699.t00001 Chromosome 111013 98.0072 CTHISYYKY 699.t00001 Chromosome 11 1046 98.0005 FVDEEGEQLYM13Hg2.q1t3 8 98.0073 NSLYNKIEY M13Hg2.q1t3 46 98.0006 YSSASESNFYM13Hg2.q1t3 49 98.0074 ASESNFYKY M13Hg2.q1t3 196 98.0075 ASGKLFSLYM13Hg2.q1t3 237 98.0076 GSNKVSDWY M13Hg2.q1t3 511 98.0007 FQDNYLKLDYM13Hg2.q1t3 597 98.0008 FFDYNSQYYY M13Hg2.q1t3 597 98.0077 FFDYNSQYYM13Hg2.q1t3 699 98.0078 MLEQKLSNY M13Hg2.q1t3 882 98.0079 NSFNNSNIYMal_5L10c4.q1t6 8 98.0080 CSSTKDLNY Mal_5L10c4.q1t6 263 98.0081YDDDKYNKY Mal_5L10c4.q1t6 638 98.0082 GTYGNMENY Mal_5L10c4.q1t6 69098.0083 FTYYSCKNY Mal_5L10c4.q1t6 1022 98.0084 YDERNTLVY Mal_5L10c4.q1t61387 98.0085 STDDSKNVY Mal_5L10c4.q1t6 1451 98.0086 FSDDNKNLYMal_5L10c4.q1t6 1508 98.0009 YLDNELTINY Mal_5L10c4.q1t6 1709 98.0087STTSLNYHY Mal_5L10c4.q1t6 1907 98.0088 GLDLKMTLY 571.t00003 Chromosome111044 98.0010 YTFQNNNDFY 571.t00003 Chromosome11 1080 98.0089 HTNNKTSIY571.t00003 Chromosome11 1710 98.0090 FVDPNKYIY 571.t00003 Chromosome111827 98.0011 NVEAYHNDNY 571.t00003 Chromosome11 1858 98.0091 YSNNSHAEY571.t00003 Chromosome11 1905 98.0092 LTNNSSYIY 571.t00003 Chromosome112211 98.0093 SSSIYNQNY 571.t00003 Chromosome11 2476 98.0094 GSYGTFLKY571.t00003 Chromosome11 2532 98.0095 DIDKTVLHY 571.t00003 Chromosome112571 98.0012 FNDTQKKGTY MP03072 PFC0450w CAA15614 95 98.0013 LSASDEYEQYMP03072 PFC0450w CAA15614 96 98.0096 SASDEYEQY 45.t00001 Chromosomel4 1398.0014 FQAAESNERY 45.t00001 Chromosomel4 14 98.0097 QAAESNERY 45.t00001Chromosomel4 81 98.0015 ELEASISGKY 45.t00001 Chromosomel4 82 98.0098LEASISGKY 45.t00001 Chromosomel4 188 98.0099 NLALLYGEY MP03137 PFC0700cCAB11150 14 98.0100 SSPLFNNFY MP03137 PFC0700c CAB11150 69 98.0101LNEQLIYTY MP03137 PFC0700c CAB11150 145 98.0102 QNADKNFLY MP03137PFC0700c CAB11150 255 98.0016 FVSSIFISFY MP03137 PFC0700c CAB11150 25698.0103 VSSIFISFY 12.t00018 Chromosome14 112 98.0104 YSYYEPLRY 12.t00018Chromosome14 250 98.0017 KSNNIIPLLY 12.t00018 Chromosome14 467 98.0105SSSDEENLY 12.t00018 Chromosome14 468 98.0106 SSDEENLYY 12.t00018Chromosome14 607 98.0107 KSNMNNNLY 12.t00018 Chromosome14 626 98.0108FYDKRFIFY 12.t00018 Chromosome14 696 98.0018 NVEKNFLLYY 12.t00018Chromosome14 696 98.0109 NVEKNFLLY 12.t00018 Chromosome14 949 98.0110KMDSFLNVY 12.t00018 Chromosome14 1042 98.0111 NSLIEFLFY mal_BU121g9.q1c180 98.0112 ATYKNGNIY mal_9A57b11.q1t2 226 98.0113 DEEKIFVKYmal_BL50e8.p1ca_5 86 98.0114 HTSNDSGSY mal_BL50e8.p1ca_5 136 98.0019FSFTVGEGKY mal_BL50e8.p1ca_5 186 98.0115 ETNNNLFIY mal_BL50e8.p1ca_5 31998.0116 HVSKHAFEY mal_BL50e8.p1ca_5 387 98.0117 MSGYSSNNYmal_BL50e8.p1ca_5 460 98.0118 FMESAFVNY mal_BL50e8.p1ca_5 650 98.0119RSPCSHKLY mal_BL50e8.p1ca_5 679 98.0020 FTGENNIERY mal_BL50e8.p1ca_5 77798.0120 NTLMLKADY mal_BL50e8.p1ca_5 880 98.0121 VSSKPANEY M13S8h6.p1t_357 98.0122 ITYSFTVSY M13S8h6.p1t_3 233 98.0123 LVETLDNLY M13S8h6.p1t_3235 98.0124 ETLDNLYLY M13S8h6.p1t_3 295 98.0125 LSAKYYISY M13S8h6.p1t_3551 98.0126 HSDIHLLNY M13S8h6.p1t_3 676 98.0021 FTSPVNIKEY M13S8h6.p1t_3746 98.0127 YSSYSSPKY M13S8h6.p1t_3 898 98.0128 GMERNKTKY M13S8h6.p1t_31268 98.0129 YSNIDSGKY M13S8h6.p1t_3 1488 98.0130 LIDLSCIHY 585.t00002Chromosome11 297 98.0131 CSDSSLNIY 585.t00002 Chromosome11 381 98.0132VSFDNNENY 585.t00002 Chromosome11 465 98.0022 YTDIIINIRY 585.t00002Chromosome11 575 98.0023 LSNIRKPLFY 585.t00002 Chromosome11 741 98.0133NVDANYCKY 585.t00002 Chromosome11 1021 98.0134 CVEKNNMSY 585.t00002Chromosome11 1161 98.0135 SSDGKKSEY 585.t00002 Chromosome11 1219 98.0136RSNNFFFSY 585.t00002 Chromosome11 1361 98.0024 FTMVYEKIKY 585.t00002Chromosome11 1739 98.0137 NVDIFLHYY 1223.t00015 mal_9A21f9.q1t_4 38798.0138 SSNEIHNFY 1223.t00015 mal_9A21f9.q1t_4 1065 98.0139 GTKLNRTKY1223.t00015 mal_9A21f9.q1t_4 1583 98.0025 ATVSRAGIVY 1223.t00015mal_9A21f9.q1t_4 1833 98.0140 YTLSSGTKY 1223.t00015 mal_9A21f9.q1t_42309 98.0141 VSEKEQQLY 1223.t00015 mal_9A21f9.q1t_4 2426 98.0142VVDFERLRY 1223.t00015 mal_9A21f9.q1t_4 2778 98.0143 FIDLYKQMY1223.t00015 mal_9A21f9.q1t_4 3445 98.0144 IVDITNVNY 1223.t00015mal_9A21f9.q1t_4 4163 98.0145 LEDVKKILY 1223.t00015 mal_9A21f9.q1t_44267 98.0146 SLDIPDIAY 599.t00001 Chromosome11 26 98.0147 SSCQNSLNY599.t00001 Chromosome11 183 98.0148 KSDITNLNY 599.t00001 Chromosome11304 98.0149 ETNNGDLKY 599.t00001 Chromosome11 430 98.0150 LSEDNKNRY599.t00001 Chromosome11 1018 98.0026 LLDLRKNGLY 599.t00001 Chromosome111412 98.0027 GVDKSLKIMY 599.t00001 Chromosome11 1427 98.0151 YTPTNKEMY599.t00001 Chromosome11 1516 98.0028 ESANDSTNYY 599.t00001 Chromosome111662 98.0152 LSNSITVSY 599.t00001 Chromosome11 1902 98.0153 GTTQSNNIYMP01072 M1045c5.p1c.C_6 27 98.0154 SDDEIIIIY MP01072 M1045c5.p1c.C_6 4198.0155 ISSNGKLNY MP01072 M1045c5.p1c.C_6 60 98.0156 GSIQNAYLY MP01072M1045c5.p1c.C_6 381 98.0157 GTMRNRKKY MP01072 M1045c5.p1c.C_6 70798.0158 KSLLKNYNY MP01072 M1045c5.p1c.C_6 725 98.0159 NVEDTNMLY MP01072M1045c5.p1c.C_6 1065 98.0029 NTDNKDVLNY MP01072 M1045c5.p1c.C_6 125398.0160 HTITISQKY MP01072 M1045c5.p1c.C_6 1257 98.0161 ISQKYTSSY MP01072M1045c5.p1c.C_6 1336 98.0030 KTFHRILAVY PIR2 T28161 228 98.0162KTNGAEERY PIR2 T28161 293 98.0163 GTVPTNLDY PIR2 T28161 403 98.0031ESSQNSPKNY PIR2 T28161 639 98.0032 QTDFQGWGHY PIR2 T28161 899 98.0164EADFIKKMY PIR2 T28161 917 98.0165 ATICRAMKY PIR2 T28161 1192 98.0033KTDEQYNENY PIR2 T28161 1201 98.0034 YTFKNPPPQY PIR2 T28161 1884 98.0166WLEYFLDDY PIR2 T28161 2221 98.0167 ITSSSESEY 55.t00004 Chromosome14 4598.0168 YVDIGSNIY 55.t00004 Chromosome14 457 98.0169 DTCKNIWNY 55.t00004Chromosome14 563 98.0170 LSQGKKNTY 55.t00004 Chromosome14 928 98.0171NIDCVISPY 55.t00004 Chromosome14 953 98.0172 NMDNLLFTY 55.t00004Chromosome14 1105 98.0035 FVDHNYNYNY 55.t00004 Chromosome14 1261 98.0173HSKENQQKY 55.t00004 Chromosome14 1339 98.0174 VSEGYTSTY 55.t00004Chromosome14 1358 98.0175 FMDSQNGMY 55.t00004 Chromosome14 1537 98.0036NSYNDSLINY 13.t00011 Chromosome14 27 98.0176 STGINEENY 13.t00011Chromosome14 44 98.0177 MNETVFLDY 13.t00011 Chromosome14 77 98.0178LTSKVWDTY 37.t00002 Chromosome14 10 98.0179 KHDALTYMY 37.t00002Chromosome14 14 98.0180 LTYMYCVYY 674.t00001 Chromosome11 201 98.0181NIDINDLGY 674.t00001 Chromosome11 260 98.0182 ISSNQFNNY 674.t00001Chromosome11 400 98.0183 DIEPLISSY 674.t00001 Chromosome11 453 98.0037VTNNDSINNY 674.t00001 Chromosome11 772 98.0184 ESGKNMEHY 674.t00001Chromosome11 868 98.0185 LKDFDMLLY 674.t00001 Chromosome11 936 98.0186YIDVEDDDY 674.t00001 Chromosome11 1001 98.0187 DMDDNYYLY 674.t00001Chromosome11 1224 98.0188 YGDNNKDCY 674.t00001 Chromosome11 1239 98.0189IYDFNNNSY PIC Malaria A*0101 A*2402 locus AA PIC A*0201 A*1101 PIC331.t00003 9 15.962 1000000.0 1475.7 1000000.0 331.t00003 9 10.6241000000.0 34.6 1000000.0 331.t00003 9 6.439 1000000.0 51.0 1000000.0331.t00003 9 5.246 1000000.0 1000000.0 1000000.0 331.t00003 9 8.7861000000.0 39035.2 242.6 331.t00003 9 18.802 1000000.0 1000000.0 1753.1331.t00003 10 9.498 1000000.0 153.7 1000000.0 331.t00003 9 4.1611000000.0 4680.1 1000000.0 331.t00003 9 18.299 1000000.0 11308.41000000.0 331.t00003 9 19.200 1000000.0 4533.0 1000000.0 18.000811 96.117 1000000.0 40.5 1000000.0 MY924Fe3.p1t1 9 4.901 1000000.0 2464.41000000.0 MY924Fe3.p1t1 10 8.740 1000000.0 445.2 1000000.0 MY924Fe3.p1t19 7.960 1000000.0 22156.1 1000000.0 MY924Fe3.p1t1 9 6.978 1000000.0117.2 1000000.0 MY924Fe3.p1t1 9 4.429 1000000.0 243.3 1000000.0MY924Fe3.p1t1 9 6.022 1000000.0 82.2 1000000.0 MY924Fe3.p1t1 9 2:1451000000.0 264.3 1000000.0 MY924Fe3.p1t1 9 3.307 1000000.0 8368.71000000.0 MY924Fe3.p1t1 9 2.218 1000000.0 4308.8 1000000.0 MY924Fe3.p1t19 2.560 1000000.0 10911.0 1000000.0 MP03001 9 1.370 1000000.0 698.41000000.0 MP03001 9 18.149 1000000.0 150075.4 1000000.0 1369.t00001 99.966 1000000.0 224.2 1019.1 1369.t00001 9 18.117 1000000.0 15763.11000000.0 1369.t00001 9 6.934 1000000.0 6419.6 1000000.0 1369.t00001 917.546 1000000.0 48.4 1000000.0 1369.t00001 9 16.912 1000000.0 1000000.01000000.0 1369.t00001 10 18.838 1000000.0 3608.2 1000000.0 1369.t00001 919.642 1000000.0 1000000.0 1000000.0 699.t00001 9 19.647 1000000.097274.6 1000000.0 699.t00001 10 1.491 1000000.0 319.3 1000000.0699.t00001 9 15.998 1000000 0 1000000.0 1000000.0 699.t00001 9 6.9081000000.0 1357.8 2826.7 699.t00001 9 11.791 1000000.0 4626.8 1000000.0699.t00001 9 12.867 1000000.0 52350.4 1000000.0 699.t00001 9 13.1591000000.0 1000000.0 1000000.0 699.t00001 9 7.495 1000000.0 22.41000000.0 699.t00001 9 14.092 1000000.0 406.1 1000000.0 699.t00001 106.559 1000000.0 5771.7 1000000.0 M13Hg2.q1t3 9 19.553 1000000.0 3889.91000000.0 M13Hg2.q1t3 10 12.365 1000000.0 5058.0 1000000.0 M13Hg2.q1t3 91.848 1000000.0 630.5 1000000.0 M13Hg2.q1t3 9 2.466 1000000.0 266.91000000.0 M13Hg2.q1t3 9 16.782 1000000.0 1646.1 1000000.0 M13Hg2.q1t3 107.493 1000000.0 19742.1 1000000.0 M13Hg2.q1t3 10 19.854 1000000.1 2749.21043.1 M13Hg2.q1t3 9 11.735 1000000.0 3766.2 160.3 M13Hg2.q1t3 9 1.2041000000.0 13925.8 1000000.0 M13Hg2.q1t3 9 16.821 1000000.0 5231.61000000.0 Mal_5L10c4.q1t6 9 2.097 1000000.0 16168.9 1000000.0Ma1_5L10c4.q1t6 9 7.997 1000000.0 98918.2 1000000.0 Mal_5L10c4.q1t6 92.825 1000000.0 209.0 1000000.0 Mal_5L10c4.q1t6 9 6.979 1000000.0 257.71000000.0 Mal_5L10c4.q1t6 9 5.181 1000000.0 47876.1 1000000.0Mal_5L10c4.q1t6 9 4.783 1000000.0 2220.4 1000000.0 Mal_5L10c4.q1t6 92.622 1000000.0 56737.7 1000000.0 Mal_5L10c4.q1t6 10 6.162 1000000.07177.6 1000000 0 Mal_5L10c4.q1t6 9 7.670 1000000.0 19.1 1000000.0Mal_5L10e4.q1t6 9 2.747 1000000.0 5170.0 1000000.0 571.t00003 10 2.1791000000.0 93.5 1000000.0 571.t00003 9 4.189 1000000.0 1677.3 1000000.0571.t00003 9 2.171 1000000.0 6898.3 1000000.0 571.t00003 10 5.8351000000.0 1804.6 1000000.0 571.t00003 9 7.282 1000000.0 662.3 1000000.0571.t00003 9 7.415 1000000.0 186.2 1000000.0 571.t00003 9 6.3301000000.0 318.5 1000000.0 571.t00003 9 1.127 1000000.0 151.7 1000000.0571.t00003 9 4.678 1000000.0 10960.5 1000000.0 571.t00003 10 7.6681000000.0 1000000.0 1000000.0 MP03072 10 14.664 1000000.0 11938.71000000.0 MP03072 9 16.603 1000000.0 163.8 1000000.0 45.t00001 10 13.6671000000.0 5804.6 1000000.0 45.t00001 9 7.537 1000000.0 4581.2 1000000.045.t00001 10 17.550 1000000.0 30954.5 1000000.0 45.t00001 9 18.2081000000.0 1000000.0 1000000.0 45.t00001 9 12.836 1000000.0 4104.61000000.0 MP03137 9 20.002 1000000.0 464.0 1000000.0 MP03137 9 10.4361000000.0 1000000.0 1000000.0 MP03137 9 10.234 1000000.0 1000000.01000000.0 MP03137 10 10.460 1000000.0 44.6 1000000.0 MP03137 9 15.7321000000.0 544.5 1000000.0 12.t00018 9 4.229 1000000.0 560.9 1000000.012.t00018 10 8.533 1000000.0 967.3 1000000.0 12.t00018 9 8.006 1000000.02243.6 1000000.0 12.t00018 9 6.105 1000000.0 64.6 1000000.0 12.t00018 96.927 1000000.0 923.1 1000000.0 12.t00018 9 4.639 1000000.0 1000000.018.3 12.t00018 10 7.724 1000000.0 328.7 1000000.0 12.t00018 9 0.7891000000.0 1330.7 1000000.0 12.t00018 9 6.016 1000000.0 1384.3 151.912.t00018 9 9.105 1000000.0 774.9 1000000.0 mal_BU121g9.q1c1 9 3.4231000000.0 290.6 1000000.0 mal_9A57b11.q1t2 9 18.436 1000000.0 1000000.01000000.0 mal_BL50e8.p1ca_5 9 7.801 1000000.0 10632.6 1000000.0mal_BL50e8.p1ca_5 10 4.464 1000000.0 4191.1 1000000.0 mal_BL50e8.p1ca_59 3.940 1000000.0 574.3 1000000.0 mal_BL50e8.p1ca_5 9 3.473 1000000.0286.4 1000000.0 mal_BL50e8.p1ca_5 9 4.983 1000000.0 1178.7 1000000.0mal_BL50e8.p1ca_5 9 2.609 1000000.0 3568.1 1208.1 mal_BL50e8.p1ca_5 96.243 1000000.0 805.6 1000000.0 mal_BL50e8.p1ca_5 10 15.909 1000000.01908.1 1000000.0 mal_BL50e8.p1ca_5 9 15.648 1000000.0 6774.7 1000000.0mal_BL50e8.p1ca_5 9 15.176 1000000.0 3405.9 1000000.0 M13S8h6.p1t_3 910.960 1000000.0 25.1 1000000.0 M13S8h6.p1t_3 9 3.907 1000000.0 24044.71000000.0 M13S8h6.p1t_3 9 2.901 1000000.0 801.6 1000000.0 M13S8h6.p1t_39 4.669 1000000.0 635.7 1000000.0 M13S8h6.p1t_3 9 1.423 1000000.0 5008.91000000.0 M13S8h6.p1t_3 10 10.972 1000000.0 1911.2 1000000.0M13S8h6.p1t_3 9 5.286 1000000.0 6184.9 1000000.0 M13S8h6.p1t_3 9 7.2441000000.0 88038.7 24764.5 M13S8h6.p1t_3 9 11.517 1000000.0 14325.61000000.0 M13S8h6.p1t_3 9 3.960 1000000.0 1722.8 1000000.0 585.t00002 92.643 1000000.0 44436.7 1000000.0 585.t00002 9 7.080 1000000.0 824.41000000.0 585.t00002 10 1.851 1000000.0 1716.6 1000000.0 585.t00002 105.132 1000000.0 3669.8 1000000.0 585.t00002 9 3.822 1000000.0 813.11000000.0 585.t00002 9 6.497 1000000.0 33246.6 1000000 0 585.t00002 95.530 1000000.0 8369.5 1000000.0 585.t00002 9 6.117 1000000.0 11.91000000.0 585.t00002 10 2.669 1000000.0 726.8 1000000.0 585.t00002 93.691 1000000.0 42.6 1000000.0 1223.t00015 9 7.488 1000000.0 19.51000000.0 1223.t00015 9 6.438 1000000.0 9805.4 1000000.0 1223.t00015 109.716 1000000.0 351.9 1000000.0 1223.t00015 9 4.847 1000000.0 1878.11000000.0 1223.t00015 9 6.585 1000000.0 56024.7 1000000.0 1223.t00015 93.185 1000000.0 457.2 1000000.0 1223.t00015 9 5.792 1000000.0 14889.51000000.0 1223.t00015 9 6.389 1000000.0 1065.1 1000000.0 1223.t00015 99.183 1000000.0 1000000.0 1000000.0 1223.t00015 9 9.566 1000000.0 1095.41000000.0 599.t00001 9 1.030 1000000.0 86.7 1000000.0 599.t00001 9 4.9231000000.0 947.1 1000000.0 599.t00001 9 6.392 1000000.0 6561.2 1000000.0599.t00001 9 7.171 1000000.0 178412.8 1000000.0 599.t00001 10 3.6961000000.0 12286.3 1000000.0 599.t00001 10 8.185 1000000.0 3010.41000000.0 599.t00001 9 6.553 1000000.0 73406.9 1000000.0 599.t00001 106.672 1000000.0 2007.1 1000000.0 599.t00001 9 9.278 1000000.0 771.61000000.0 599.t00001 9 3.444 1000000.0 4003.2 1000000.0 MP01072 9 11.3591000000.0 1265.6 1000000.0 MP01072 9 6.926 1000000.0 2877.4 1000000.0MP01072 9 2.697 1000000.0 389.5 1000000.0 MP01072 9 1.998 1000000.0249.1 1000000.0 MP01072 9 15.958 1000000.0 419.1 1000000.0 MP01072 99.314 1000000.0 3255.4 1000000.0 MP01072 10 6.923 1000000.0 6127.01000000.0 MP01072 9 3.528 1000000.0 4947.2 1000000.0 MP01072 9 13.1571000000.0 5019.1 1000000.0 MP01072 10 13.836 1000000.0 85.1 1000000.0PIR2 9 8.691 1000000.0 326.3 1000000.0 PIR2 9 3.979 I000000.0 793.41000000.0 PIR2 10 8.536 1000000.0 24883.8 1000000.0 PIR2 10 2.6011000000.0 1349.4 1000000.0 PIR2 9 9.348 1000000.0 113941.0 1000000.0PIR2 9 5.412 1000000.0 112.4 1000000.0 PIR2 10 5.386 1000000.0 1911.81000000.0 PIR2 10 8.064 1000000.0 918.8 1000000.0 PIR2 9 8.602 1000000.035096.0 1000000.0 PIR2 9 9.299 1000000.0 1168.0 1000000.0 55.t00004 93.352 1000000.0 18704.2 1000000.0 55.t00004 9 3.842 1000000.0 878.31000000.0 55.t00004 9 10.561 1000000.0 40514.9 1000000.0 55.t00004 98.449 1000000.0 3464.1 1000000.0 55.t00004 9 5.144 1000000.0 413.36464.5 55.t00004 10 6.601 1000000.0 687.9 1000000.0 55.t00004 9 3.7981000000.0 41445.3 1000000.0 55.t00004 9 7.735 1000000.0 4760.1 1000000.055.t00004 9 8.455 1000000.0 21913.6 2720.6 55.t00004 10 12.536 1000000.01846.9 1000000.0 13.t00011 9 6.590 1000000.0 838.9 1000000.0 13.t00011 95.456 1000000.0 1000000.0 1000000.0 13.t00011 9 6.496 1000000.0 616.61000000.0 37.t00002 9 23.541 1000000.0 1000000.0 1000000.0 37.t00002 910.044 1000000.0 20.3 1000000.0 674.t00001 9 10.069 1000000.0 23874.21000000.0 674.t00001 9 6.099 1000000.0 2575.9 1000000.0 674.t00001 914.646 1000000.0 183727.1 1000000.0 674.t00001 10 17.920 1000000.01310.7 1000000.0 674.t00001 9 8.198 1000000.0 75390.5 1000000.0674.t00001 9 12.047 1000000.0 1000000.0 1000000.0 674.t00001 9 13.8701000000.0 377275.0 1000000.0 674.t00001 9 3.056 1000000.0 2478.6 45380.9674.t00001 9 19.772 1000000.0 368191.0 1000000.0 674.t00001 9 17.7351000000.0 1000000.0 365.4

TABLE 3 Pf-derived A24 supertype peptides with PIC < 100 nM PICMalaria locus Addn Source info Accession No. Position Peptide No.Sequence AA A*0101 PIC A*0201 A*1101 A*2402 PIC 331.t00003 Chromosome1010 98.0206 FYKKKRNVL 9 67134.0 1000000.0 1000000.0 1.708 331.t00003Chromosome10 110 98.0207 VYEINKNEF 9 84.1 1000000.0 1000000.0 2.011331.t00003 Chromosome10 604 98.0208 FFVWGIIDMF 9 221.0 1000000.01000000.0 3.642 331.t00003 Chromosome10 684 98.0209 VYNIKENFW 9 123239.41000000.0 1000000.0 2.687 331.t00003 Chromosome10 1108 98.0210KYNLCIINML 9 147073.6 1000000.0 1000000.0 0.324 331.t00003 Chromosome101268 98.0211 FYVPIKKKL 9 172677.3 1000000.0 1000000.0 2.705 331.t00003Chromosome10 1365 98.0212 KYEIIGNIL 9 89209.4 1000000.0 1000000.0 1.961331.t00003 Chromosome10 1449 98.0213 FWLAIKDIF 9 173.9 1000000.01000000.0 1.093 331.t00003 Chromosome10 1515 98.0214 LYRRRKNLF 9 113.51000000.0 1000000.0 1.220 331.t00003 Chromosome10 1704 98.0215 IYIIKQNSF9 111.6 1000000.0 1000000.0 0.256 18.000811 Chr12Contig18 5 98.0190LFVCFLIFHF 10 672.3 1000000.0 1000000.0 19.783 18.000811 Chr12Contig18 898.0191 CFLIFHFFLF 10 1385.7 1000000.0 1000000.0 18.444 18.000811Chr12Contig18 8 98.0216 CFLIFHFFL 9 106491.6 1000000.0 1000000.0 0.32118.000811 Chr12Contig18 11 98.0217 IFHFFLFLL 9 53306.2 1000000.01000000.0 38.527 18.000811 Chr12Contig18 13 98.0192 HFFLFLLYIL 101000000.0 1000000.0 1000000.0 35.659 18.000811 Chr12Contig18 13 98.0218HFFLFLLYI 9 24845.8 1000000.0 1000000.0 26.159 18.000811 Chr12Contig1814 98.0219 FFLFLLYIL 9 62569.1 1000000.0 1000000.0 32.471 18.000811Chr12Contig18 19 98.0220 LYILFLVKM 9 90645.8 1000000.0 1000000.0 63.05118.000811 Chr12Contig18 41 98.0221 VFLVFSNVL 9 178682.3 1000000.01000000.0 5.555 18.000811 Chr12Contig18 160 98.0222 TYGIIVPVL 9 123562.91000000.0 1000000.0 3.015 MY924Fe3.p1t1 153 98.0223 FFNVINIFF 9 45.61000000.0 1000000.0 0.470 MY924Fe3.p1t1 1412 98.0224 FYSWLQNVL 9 83170.31000000.0 1000000.0 2.428 MY924Fe3.p1t1 1435 98.0225 FYERFSDLI 9 46149.11000000.0 1000000.0 0.625 MY924Fe3.p1t1 1534 98.0226 VYLIQNNYI 9615175.4 1000000.0 1000000.0 0.632 MY924Fe3.p1t1 1557 98.0227 NYMKNSFYI9 24802.7 1000000.0 1000000.0 2.200 MY924Fe3.p1t1 1800 98.0228 VYCNYVTEI9 160654.7 1000000.0 1000000.0 3.071 MY924Fe3.p1t1 1839 98.0229HYEVLPYKF 9 14.6 1000000.0 1000000.0 2.621 MY924Fe3.p1t1 1846 98.0230KFTIIVESL 9 181796.5 1000000.0 1000000.0 1.946 MY924Fe3.p1t1 215998.0231 FMTRAHFHI 9 9020.6 52.2 1000000.0 1.455 MY924Fc3.p1t1 238098.0232 FYKSKVIII 9 53263.7 1000000.0 1000000.0 0.928 MP03001 MAL3P2.11CAB38998 11 98.0233 SFLFVEALF 9 80.3 1000000.0 1000000.0 53.045 MP03001MAL3P2.11 CAB38998 54 98.0234 YYGKQENWY 9 73.1 1000000.0 1000000.049.750 MP03001 MAL3P2.11 CAB38998 369 98.0235 KMEKCSSVF 9 34.0 1000000.01000000.0 39.989 MP03001 MAL3P2.11 CAB38998 376 98.0236 VFNVVNSSI 9231723.3 1000000.0 1000000.0 82.506 1369.t00001 Chromosome11 34 98.0237NYMKIMNHL 9 37582.2 1000000.0 1000000.0 4.875 1369.t00001 Chromosome11225 98.0193 SYKSSKRDKF 10 1632.7 1000000.0 1000000.0 46.746 1369.t00001Chromosome11 264 98.0238 TYKKKNNHI 9 90904.7 1000000.0 1000000.0 12.0421369.t00001 Chromosome11 277 98.0239 VYYNILIVL 9 59837A 1000000.01000000.0 11.637 1369.t00001 Chromosome11 285 98.0240 LYYLFNQHI 956431.2 1000000.0 1000000.0 5.598 1369.t00001 Chromosome11 310 98.0241SFFMNRFYI 9 56480.3 1000000.0 1000000.0 80.940 1369.t00001 Chromosome11316 98.0242 FYITTRYKY 9 45.2 1000000.0 1000000.0 3.968 1369.t00001Chromosome11 328 98.0243 KYINFINFI 9 289163.4 1000000.0 1000000.0 0.0951369.t00001 Chromosome11 331 98.0244 NFINFIKVL 9 610070.5 1000000.01000000.0 37.188 1369.t00001 Chromosome11 380 98.0245 KYEALIKLL 9105887.8 1000000.0 1000000.0 9.605 699.t00001 Chromosome11 443 98.0246FFFSLIDYF 9 118.9 1000000.0 1000000.0 1.331 699.t00001 Chromosome11 46098.0247 KYNIKVCEL 9 98354.1 1000000.0 1000000.0 0.429 699.t00001Chromosome11 487 98.0248 FYLYISFLL 9 34312.8 1000000.0 1000000.0 0.417699.t00001 Chromosome11 664 98.0249 FYTNNANLL 9 42910.8 1000000.01000000.0 0.639 699.t00001 Chromosome11 766 98.0250 EYNPSFFYL 9 22929.41000000.0 1000000.0 1.772 699.t00001 Chromosome11 845 98.0251 SFIIFKNIF9 249.9 1000000.0 1000000.0 3.449 699.t00001 Chromosome11 881 98.0252LYMNFLKFI 9 34148.2 1000000.0 1000000.0 4.363 699.t00001 Chromosome11929 98.0253 KYLIILLYI 9 93640.1 1000000.0 1000000.0 1.034 699.100001Chromosome11 1020 98.0254 KYIYIYIYI 9 215740.5 1000000.0 1000000.0 0.296699.100001 Chromosome11  1024 98.0255 IYIYIFIYL 9 52331.1 1000000.01000000.0 2.300 M13Hg2.q1t3 135 98.0256 IYINKLSFF 9 67.4 1000000.01000000.0 3.329 M13Hg2.q1t3 142 98.0257 FFSIKDELF 9 27.2 1000000.01000000.0 14.276 M13Hg2.q1t3 156 98.0258 EFLKNNSYF 9 164.9 1000000.01000000.0 20.204 M13Hg2.q1t3 163 98.0259 YFNIIQQKI 9 45274.1 1000000.01000000.0 13.888 M13Hg2.q1t3 244 98.0260 WYCSACNFL 9 56993.5 1000000.01000000.0 7.339 M13Hg2.q1t3 296 98.0261 LYLINNKNL 9 150801.1 1000000.01000000.0 28.854 M13Hg2.q1t3 345 98.0262 TYKDANNNI 9 71978.1 1000000.01000000.0 29.035 M13Hg2.q113 521 98.0263 VYEKEKQYF 9 103.6 1000000.01000000.0 3.963 M13Hg2.q1t3 553 98.0194 PYFNFFVNYF 10 185.8 1000000.01000000.0 33.503 M13Hg2.q1t3 889 98.0264 IYNNNNEHI 9 77962.6 1000000.01000000.0 24.919 Mal_5L10c4.q1t6 78 98.0265 EYNKYNEYF 9 90.4 1000000.01000000.0 3.130 Mal_5L10c4.q1t6 137 98.0266 NYVNNNNVF 9 220.5 1000000.01000000.0 3.441 Mal_5L10c4.q1t6 321 98.0267 KYPIKYCEL 9 183114.81000000.0 1000000.0 0.364 Mal_5L10c4.q1t6 416 98.0268 AYHDLIKLF 9 66.81000000.0 1000000.0 4.671 Mal_5L10c4.q116 533 98.0269 KYISSVNYF 9 194.81000000.0 1000000.0 0.018 Mal_5L10c4.q1t6 773 98.0270 KYDWFFNSF 9 34.01000000.0 1000000.0 0.374 Mal_5L10c4.q1t6 1183 98.0271 HYVIKKYII 9133499.1 1000000.0 1000000.0 1.507 Mal_5L10c4.q1t6 1259 98.0272LYLHIHKLF 9 72.0 1000000.0 1000000.0 0.343 Mal_5L10c4.q1t6 1323 98.0273YYRTNYGYI 9 165642.6 1000000.0 1000000.0 4.072 Mal_5L10c4.q1t6 205498.0274 KYLRYHSQL 9 421667.1 1000000.0 1000000.0 0.655 571.t00003Cluomosome11 74 98.0275 FYIDKCIHF 9 23.2 1000000.0 1000000.0 0.120571.t00003 Chromosome11 162 98.0276 FYTNYYQSF 9 48.3 1000000.0 1000000.00.186 571.t00003 Chromosome11 177 98.0277 PYINQTNIF 9 228.9 1000000.01000000.0 0.527 571.t00003 Chromosome11 807 98.0278 NYPNNANHI 9 176667.01000000.0 1000000.0 3.103 571.t00003 Chromosome11 834 98.0279 TYNNFHNSY9 52.4 1000000.0 1000000.0 0.776 571.t00003 Chromosome11 1917 98.0280YMNNNTYSF 9 7.7 1000000.0 1000000.0 2.132 571.t00003 Chromosome11 202698.0281 KYTEGATNF 9 74.8 1000000.0 1000000.0 1.964 571.t00003Chromosome11 2450 98.0282 FYISIIDII 9 150563.0 1000000.0 1000000.0 1.632571.t00003 Chromosome11 2540 98.0283 YYKEHISEF 9 96.3 1000000.01000000.0 3.143 571.t00003 Chromosome11 2914 98.0284 YYNRANNEI 9 46291.41000000.0 1000000.0 3.342 MP03072 PFC0450w CAA15614 17 98.0285 AFLLITFLM9 37258.4 1000000.0 1000000.0 17.525 MP03072 PFC0450w CAA15614 5398.0195 LYVIFLVLLF 10 174.0 1000000.0 1000000.0 16.581 MP03072 PFC0450wCAA15614 53 98.0286 LYVIFLVLL 9 107336.6 1000000.0 1000000.0 5.089MP03072 PFC0450w CAA15614 86 98.0287 KYVQLASTY 9 65.1 1000000.01000000.0 70.547 45.t00001 Chromosome14 21 98.0196 RYQDPQNYEL 101000000.0 1000000.0 1000000.0 46.471 45.t00001 Chromosome14 40 98.0288IYYEDGNSW 9 97026.0 1000000.0 1000000.0 15.493 45.t00001 Chromosome14 9498.0289 VYRHCEYIL 9 560574.8 1000000.0 1000000.0 27.538 45.t00001Chromosome14 135 98.0290 TWKPTIFLL 9 34068.5 1000000.0 1000000.0 26.74145.t00001 Chromosome14 168 9830291 SYKVNCINF 9 25.3 1000000.0 1000000.063.592 45.t00001 Chromosome14 216 98.0292 KYNYFIHFF 9 39.1 1000000.01000000.0 0.380 45.t00001 Chromosome14 218 98.0293 NYFIHFFTW 9 95820.51000000.0 1000000.0 2.156 45.t00001 Chromosome14 222 98.0294 HFFTWGTMF 917.4 1000000.0 1000000.0 6.418 45.t00001 Chromosome14 229 98.0295MFVPKYFEL 9 57423.3 1000000.0 1000000.0 28.589 45.t00001 Chromosome14295 98.0296 IYTIIQDQL 9 334935.0 1000000.0 1000000.0 9.774 MP03137PFC0700c CAB11150 3 98.0197 DFFLKSKFNI 10 1000000.0 1000000.0 1000000.079.527 MP03137 PFC0700c CAB11150 4 98.0297 FFLKSKFNI 9 80470.7 1000000.01000000.0 10.043 MP03137 PFC0700c CAB11150 9 98.0298 KFNILSSPL 9275819.0 1000000.0 1000000.0 48.661 MP03137 PFC0700c CAB11150 61 98.0299RMTSLKNEL 9 45471.5 1089.6 1000000.0 50.292 MP03137 PFC0700c CAB11150 7798.0300 YYNNFNNNY 9 29.9 1000000.0 1000000.0 2.802 MP03137 PFC0700cCAB11150 87 98.0301 YYNKSTEKL 9 25069.1 1000000.0 1000000.0 6.131MP03137 PFC0700c CAB11150 109 98.0302 EYEPTANLL 9 29899.8 1000000.01000000.0 9.359 12.t00018 Chromosome14 479 98.0303 PYEEVENYF 9 118.21000000.0 1000000.0 3.525 12.t00018 Chromosome14 506 98.0304 KFILHMTLL 9418744.3 1000000.0 1000000.0 7.942 12.t00018 Chromosome14 544 98.0305NFLNIYASL 9 309896.9 1000000.0 1000000.0 7.653 12.t00018 Chromosome14594 98.0306 VWKKLIEYF 9 120.2 1000000.0 1000000.0 7.058 12.t00018Chromosome14 614 98.0307 LYVSMYIPF 9 113.5 1000000.0 1000000.0 6.67912.t00018 Chromosome14 618 98.0308 MYIPFIKKF 9 62.3 1000000.0 1000000.02.663 12.t00018 Chromosome14 625 98.0309 KFYDKRFIF 9 53.3 1000000.01000000.0 1.395 12.t00018 Chromosome14 675 98.0310 IYNMYHNNF 9 27.21000000.0 1000000.0 0.737 12.t00018 Chromosome14 678 98.0311 MYHNNFSYF 961.8 1000000.0 1000000.0 5.105 12.t00018 Chromosome14 815 98.0312KYDITKNLI 9 86746.4 1000000.0 1000000.0 2.983 mal_BU121g9.q1c1 6198.0313 GYFKRIFKL 9 39278.5 1000000.0 1000000.0 64.889 mal_BU121g9.q1c181 98.0314 TYKNGNIYI 9 240142.1 1000000.0 1000000.0 20.110mal_BU121g9.q1c1 87 98.0315 IYIYIYIYI 9 133656.3 1000000.0 1000000.02.246 mal_BU121g9.q1c1 89 98.0198 IYIYIYIYFL 10 1000000.0 1000000.01000000.0 72.026 mal_BU121g9.q1c1 89 98.0316 IYIYIYIYF 9 89.8 1000000.01000000.0 0.543 mal_9A57b11.q1t2 75 98.0317 IFKNDNNTF 9 290.7 1000000.01000000.0 11.568 mal_9A57b11.q1t2 103 98.0318 KYGNICHHI 9 61693.11000000.0 1000000.0 4.552 mal_9A57b11.q1t2 139 98.0319 QYTDIPSLI 941835.9 1000000.0 1000000.0 24.727 mal_9A57b11.q1t2 159 98.0320VFCYEYFIF 9 98.9 1000000.0 1000000.0 69.226 mal_9A57b11.q1t2 161 98.0199CYEYFIFDIF 10 811.1 1000000.0 1000000.0 61.974 mal_9A57b11.q1t2 16198.0321 CYEYFIFDI 9 32300.1 1000000.0 1000000.0 79.659 mal_9A57b11.q1t2171 98.0322 KYARNILSL 9 27927.9 1000000.0 1000000.0 3.398mal_9A57b11.q1t2 230 98.0323 IFVKYLPLF 9 68.2 1000000.0 1000000.0 30.518mal_9A57b11.q1t2 233 98.0324 KYLPLFLMM 9 16925.5 1000000.0 1000000.015.776 mal_9A5tb11.q1t2 237 98.0325 LFLMMEIISF 9 51.0 1000000.01000000.0 70.804 mal_BL50e8.p1ca_5 116 98.0326 QYSNYFDYL 9 103941.71000000.0 1000000.0 17.499 mal_BL50e8.p1ca_5 184 98.0327 PYETNNNLF 937.2 1000000.0 1000000.0 4.367 mal_BL50e8.p1ca_5 341 98.0328 YYSRRVEKI 933168.4 1000000.0 1000000.0 6.349 mal_BL50e8.p1ca_5 555 98.0329KFKWIQDNL 9 453346.6 1000000.0 1000000.0 30.007 mal_BL50e8.p1ca_5 68798.0200 RYVGLGSFHF 10 1143.3 1000000.0 1000000.0 33.267mal_BL50e8.p1ca_5 768 98.0330 TYKMYPPEF 9 68.2 1000000.0 1000000.0 7.746mal_BL50e8.p1ca_5 771 98.0331 MYPPEFNTL 9 37286.8 1000000.0 1000000.014.291 mal_BL50e8.p1ca_5 827 98.0332 KYCIGSTYF 9 184.3 1000000.01000000.0 0.261 mal_BL50e8.plca_5 833 98.0333 TYFLRQVSI 9 163553.31000000.0 1000000.0 31.623 mal_BL50e8.p1ca_5 857 98.0334 KYSARLHPI 952609.1 1000000.0 1000000.0 33.171 M13S8h6.p1t_3 152 98.0335 FYLKKKFLF 930.5 1000000.0 1000000.0 0.091 M13S8h6.p1t_3 298 98.0336 KYYISYKVL 9328554.4 1000000.0 1000000.0 3.468 M13S8h6.p1t_3 321 98.0337 KYINKNISL 9213679.4 1000000.0 1000000.0 0.395 M13S8h6.p1t_3 380 98.0338 KYLKEDNTF 9189.5 1000000.0 1000000.0 2.580 M13S8h6.p1t_3 753 98.0339 KYGDNENNF 950.4 1000000.0 1000000.0 2.048 M13S8h6.p1t_3 1208 98.0340 VFTKINNLF 955.7 1000000.0 1000000.0 4.101 M13S8h6.p1t_3 1438 98.0341 IWLIRSIYL 9175087.7 1000000.0 1000000.0 2.659 M13S8h6.p1t_3 1444 98.0342 IYLFIITYI9 153399.4 1000000.0 1000000.0 4.385 M13S8h6.p1t_3 1536 98.0343FFFVFFYIF 9 26.2 1000000.0 1000000.0 0.631 M13S8h6.p1t_3 1541 98.0344FYIFLIYSF 9 60.5 1000000.0 1000000.0 0.315 585.t00002 Chromosome11 198.0345 MYIFFFILF 9 12.6 1000000.0 1000000.0 1.911 585.t00002Chromosome11 11 98.0346 FYVMSTYTF 9 45.7 1000000.0 1000000.0 0.144585.t00002 Chromosome11 512 98.0347 RYCTKCFLW 9 31357.1 1000000.01000000.0 1.726 585.t00002 Chromosome11 605 98.0348 VYAKNIPLW 9 36459.41000000.0 1000000.0 1.882 585.t00002 Chromosome11 663 98.0349 FFCTFFISL9 35177.1 1000000.0 1000000.0 1.436 585.t00002 Chromosome11 681 98.0350PYYKKKNLF 9 53.3 1000000.0 1000000.0 2.732 585.t00002 Chromosome11 137898.0351 FYTLVNILI 9 40959.2 1000000.0 1000000.0 2.113 585.t00002Chromosome11 1419 98.0352 YFIIRSYEL 9 135598.6 1000000.0 1000000.0 2.721585.t00002 Chromosome11 1483 98.0353 KYICLTCAF 9 30.1 1000000.01000000.0 0.435 585.t00002 Chromosome11 1752 98.0354 KYDLFNNFI 9 83062.51000000.0 1000000.0 1.355 1223.t00015 mal_9A21f9.q1t_4 1202 98.0355KYKDMAKIF 9 215.2 1000000.0 1000000.0 0.315 1223.t00015 mal_9A21f9.q1t_41599 98.0356 GYRPFIYSW 9 83421.5 1000000.0 1000000.0 3.292 1223.t00015mal_9A21f9.q1t_4 1621 98.0357 LYAIFNKLF 9 57.9 1000000.0 1000000.0 0.2121223.t00015 mal_9A21f9.q1t_4 1631 98.0358 FYLDKIQIL 9 36632.3 1000000.01000000.0 0.942 1223.t00015 mal_9A21f9.q1t_4 2272 98.0359 RMEDKTFSL 98870.6 143.4 1000000.0 4.349 1223.t00015 mal_9A21f9.q1t_4 2702 98.0360IYNCVTINW 9 10684.6 1000000.0 1000000.0 2.727 1223.t00015mal_9A21f9.q1t_4 3109 98.0361 RWTDDSNNF 9 60.4 1000000.0 1000000.0 1.6001223.t00015 mal_9A21f9.q1t_4 3735 98.0362 FFYDILNVI 9 40209.1 1000000.01000000.0 5.095 1223.t00015 mal_9A21f9.q1t_4 3968 98.0363 KYRKIIYSL 9215862.1 1000000.0 1000000.0 0.665 1223.t00015 mal_9A21f9.q1t_4 451598.0364 KYFIFRIHL 9 114989.5 1000000.0 1000000.0 0.325 599.t00001Chromosome11 8 98.0365 KYLTINFFI 9 160943.0 1000000.0 1000000.0 0.123599.t00001 Chromosome11 14 98.0366 FFILLTLVF 9 30.5 1000000.0 1000000.03.495 599.t00001 Chromosome11 24 98.0367 KYSSCQNSL 9 213208.8 1000000.01000000.0 0.906 599.t00001 Chromosome11 955 98.0368 KFIEHINEF 9 278.81000000.0 1000000.0 1.175 599.t00001 Chromosome11 1118 98.0369 KYIELNDLI9 231736.4 1000000.0 1000000.0 1.464 599.t00001 Chromosome11 119498.0370 PYSNVTYVI 9 97127.6 1000000.0 1000000.0 1.861 599.t00001Chromosome11 1434 98.0371 MYDILNAYF 9 42.0 1000000.0 1000000.0 1.204599.t00001 Chromosome11 1769 98.0372 IIYIMNNTIF 9 38.3 1000000.01000000.0 1.389 599.t00001 Chromosome11 1929 98.0373 FFKYIISYF 9 126.11000000.0 1000000.0 3.000 599.t00001 Chromosome11 1943 98.0374 KYLNDDNYL9 679247.8 1000000.0 1000000.0 0.368 MP01072 M1045c5.p1c.C_6 67 98.0375LYKSIFKAF 9 52.5 1000000.0 1000000.0 21.749 MP01072 M1045c5.p1c.C_6 10798.0376 SYRIVNAGF 9 268.7 1000000.0 1000000.0 7.480 MP01072M1045c5.p1c.C_6 319 98.0377 KYTFRSLSI 9 63496.4 1000000.0 1000000.07.958 MP01072 M1045c5.p1c.C_6 388 98.0378 KYKNDSNRI 9 401700.0 1000000.01000000.0 6.170 MP01072 M1045c5.p1c.C_6 612 98.0379 SYIYNKNIF 9 105.61000000.0 1000000.0 13.043 MP01072 M1045c5.p1c.C_6 1042 98.0380FMKNNTTLF 9 117 1000000.0 1000000.0 2.141 MP01072 M1045c5.p1c.C_6 112398.0381 HYVMINNNL 9 52910.4 1000000.0 1000000.0 3.607 MP01072M1045c5.p1c.C_6 1163 98.0382 FFLFFSIFI 9 69264.3 1000000.0 1000000.02.646 MP01072 M1045c5.p1c.C_6 1249 98.0383 RYFLHTITI 9 101443.41000000.0 1000000.0 2.834 MP01072 M1045c5.p1c.C_6 1260 98.0384 KYTSSYDSL9 230897.9 1000000.0 1000000.0 1.533 PIR2 T28161 243 98.0385 YYKLREDWW 9283854.6 1000000.0 1000000.0 8.617 PIR2 T28161 304 98.0386 QYLRWFEEW 935188.7 1000000.0 1000000.0 14.859 PIR2 T28161 628 98.0387 HWTQIKKIIF 930.8 1000000.0 1000000.0 11.497 PIR2 T28161 647 98.0388 HYFVLETVL 965432.8 1000000.0 1000000.0 12.976 PIR2 T28161 833 98.0389 RWMDTAGFI 932693.4 1000000.0 1000000.0 6.822 PIR2 T28161 848 98.0201 IYMPPRRQHF 10391.2 1000000.0 1000000.0 14.666 PIR2 T28161 1024 98.0390 RWMTEWAEW 939609.0 1000000.0 1000000.0 3.877 PIR2 T28161 1574 98.0391 KYQYDKVKL 9515925.0 1000000.0 1000000.0 6.877 PIR2 T28161 1681 98.0392 KYCRFYKRW 9239673.9 1000000.0 1000000.0 3.433 PIR2 T28161 1887 98.0393 YFLDDYNKI 9114991.6 1000000.0 1000000.0 7.588 55.t00004 Chromosome14 223 98.0394KYELRKTSI 9 226076.9 1000000.0 1000000.0 3.213 55.t00004 Chromosome14339 98.0395 MYKNKVDPL 9 208222.7 1000000.0 1000000.0 31.490 55.t00004Chromosome14 455 98.0396 YYDTCKNIW 9 80910.8 1000000.0 1000000.0 11.82055.t00004 Chromosome14 686 98.0397 KYINNMSFI 9 317672.0 1000000.01000000.0 1.757 55.t00004 Chromosome14 896 98.0398 LYPWKENKF 9 99.51000000.0 1000000.0 6.128 55.t00004 Chromosome14 973 98.0399 KWNVFNNSI 9191824.8 1000000.0 1000000.0 0.536 55.t00004 Chromosome14 1027 98.0400KFKIINSYI 9 648818.6 1000000.0 1000000.0 2.246 55.t00004 Chromosome141123 98.0401 NYAYDNIEL 9 113781.7 1000000.0 1000000.0 8.937 55.t00004Chromosome14 1155 98.0402 IYTSTNNII 9 105468.3 1000000.0 1000000.0 7.72355.t00004 Chromosome14 1268 98.0403 KYTYNINNL 9 65476.9 1000000.01000000.0 7.681 13.t00011 Chromosome14 68 98.0202 RYNVINHIYL 101000000.0 1000000.0 1000000.0 74.419 13.t00011 Chromosome14 68 98.0404RYNVINHIY 9 26.0 1000000.0 1000000.0 55.779 13.t00011 Chromosome14 8498.0405 TYNYLTPTL 9 75416.9 1000000.0 1000000.0 7.874 13.t00011Chromosome14 96 98.0203 RFRVFKDYSF 10 3387.1 1000000.0 1000000.0 29.34413.t00011 Chromosome14 99 98.0406 VFKDYSPFI 9 99598.3 1000000.01000000.0 7.373 13.t00011 Chromosome14 105 98.0407 FFIDEVKKI 9 230004.21000000.0 1000000.0 12.686 37.t00002 Chromosome14 20 98.0408 VYYDNYESL 972350.5 1000000.0 1000000.0 10.652 674.t00001 Chromosome11 68 98.0409RFVEKIYYL 9 228887.0 1000000.0 1000000.0 8.045 674.t00001 Chromosomell114 98.0410 IYINVQKNL 9 306183.0 1000000.0 1000000.0 14.033 674.t00001Chromosome11 140 98.0411 KFYYYFKEF 9 92.8 1000000.0 1000000.0 14.487674.t00001 Chromosome11 141 98.0204 EYYYFKEFLL 10 1000000.0 1000000.01000000.0 13.628 674.t00001 Chromosome11 141 98.0412 FYYYFKEFL 9104311.6 1000000.0 1000000.0 1.300 674.t00001 Chromosome11 418 98.0413TYIPDKKLL 9 209801.1 1000000.0 1000000.0 17.181 674.t00001 Chromosome11461 98.0414 NYLYNKYYI 9 288938.1 1000000.0 1000000.0 5.750 674.t00001Chromosome11 579 98.0415 NFKEQHLLF 9 72.4 1000000.0 1000000.0 38.780674.t00001 Chromosome11 649 98.0416 FIYINNKHNL 9 41447.1 1000000.01000000.0 10.887 674.100001 Chromosome11 800 98.0417 LYREIISREL 9274526.6 1000000.0 1000000.0 38.601 674.t00001 Chromosome11 1095 98.0418NYINNNIYL 9 268777.1 1000000.0 1000000.0 3.259 674.t00001 Chromosome111117 98.0419 NYNQKENSF 9 40.2 1000000.0 1000000.0 27.868 674.t00001Chromosome11 1396 98.0205 QYKVKIKPVF 10 5076.8 1000000.0 1000000.042.788

TABLE 4 Pf-derived A2 supertype peptides with PIC < 100 nM PICMalaria locus Addn Source info Position Accession No. Peptide No.Sequence AA A*0101 A*0201 PIC A*1101 A*2402 331.t00003 Chromosome10 10599.0042 LIYPCVYEI 9 38050.5 43.8 1000000.0 1000000.0 331.t00003Chromosome10 598 99.0043 NMNVQNFFV 9 50979.5 35.3 1000000.0 1000000.0331.t00003 Chromosome10 605 99.0044 FVWGHDMFM 9 25516.6 18.5 1000000.01000000.0 331.t00003 Chromosome10 660 99.0045 QLDDKFAFI 9 3138.5 43.01000000.0 1000000.0 331.t00003 Chromosome10 950 99.0046 CLINHNFFM 963467.3 65.7 1000000.0 1000000.0 331.t00003 Chromosome10 957 99.0047FMLVGGINI 9 11445.4 72.5 1000000.0 399.0 331.t00003 Chromosome10 100799.0048 YIIGGGCTV 9 19833.9 77.9 1000000.0 1000000.0 331.t00003Chromosome10 1016 99.0049 FTFGSFPDV 9 2705.2 14.1 1000000.0 1000000.0331.t00003 Chromosome10 1847 99.0050 NLSFAQYTL 9 22775.6 52.7 1000000.01000000.0 331.t00003 Chromosome10 1889 99.0051 RMYHYVVDI 9 47589.4 49.41000000.0 890.2 18.000811 Chr12Contig18 2 99.0001 VLRLFVCFLI 101000000.0 72.4 1000000.0 1000000.0 18.000811 Chr12Contig18 9 99.0002FLIFHFFLFL 10 1000000.0 10.9 1000000.0 1000000.0 18.000811 Chr12Contig1810 99.0003 LIFHFFLFLL 10 1000000.0 29.1 1000000.0 1000000.0 18.000811Chr12Contig18 15 99.0004 FLFLLYILFL 10 404264.4 19.6 1000000.0 1000000.018.000811 Chr12Contig18 32 99.0005 RLPVICSFLV 10 1000000.0 99.31000000.0 1000000.0 18.000811 Chr12Contig18 35 99.0006 VICSFLVFLV 101000000.0 71.5 1000000.0 1000000.0 18.000811 Chr12Contig18 39 99.0007FLVFLVFSNV 10 1000000.0 45.6 1000000.0 1000000.0 18.000811 Chr12Contig1810 99.0052 LIFHFFLFL 9 8592.7 9.8 1000000.0 1000000.0 18.000811Chr12Contig18 17 99.0053 FLLYILFLV 9 6742.1 1.9 1000000.0 1000000.018.000811 Chr12Contig18 35 99.0054 VICSFLVFL 9 43080.6 76.0 1000000.01000000.0 18.000811 Chr12Contig18 159 99.0055 ATYGIIVPV 9 18077.0 45.41000000.0 1000000.0 MY924Fe3.p1t1 222 99.0008 FLYAFNKYYV 10 538964.215.2 1000000.0 1000000.0 MY924Fe3.p1t1 127 99.0056 NMISVVYYI 9 97099.214.5 1000000.0 8.2 MY924Fe3.p1t1 299 99.0057 SLCFYFLLL 9 2719.7 20.91000000.0 1000000.0 MY924Fe3.p1t1 470 99.0058 ILFLHNYLL 9 31359.3 26.71000000.0 1000000.0 MY924Fe3.p1t1 512 99.0059 YLDVYNFLL 9 4353.0 7.21000000.0 1000000.0 MY924Fc3.p1t1 1209 99.0060 FQLYYMYYL 9 91212.8 4.01000000.0 1000000.0 MY924Fe3.p1t1 1267 99.0061 YVMDKVLKL 9 984.8 45.31000000.0 1000000.0 MY924Fe3.p1t1 2260 99.0062 LLFILSHFI 9 11073.4 23.71000000.0 1000000.0 MY924Fe3.p1t1 2326 99.0063 YLVNYCLVV 9 16842.3 10.91000000.0 1000000.0 MY924Fe3.p1t1 2395 99.0064 KIYVCIYYL 9 157982.7 39.31000000.0 1000000.0 MP03001 MAL3P2.11 6 CAB38998 99.0009 ILSVSSFLFV 101000000.0 94.9 1000000.0 1000000.0 MP03001 MAL3P2.11 386 CAB3899899.0010 LIMVLSFLFL 10 1000000.0 38.4 1000000.0 1000000.0 MP03001MAL3P2.11 318 CAB38998 99.0065 YLNKIQNSL 9 13496.2 78.4 1000000.01000000.0 MP03001 MAL3P2.11 387 CAB38998 99.0066 IMVLSFLFL 9 8739.3 36.01000000.0 2608.6 1369.t00001 Chromosome11 60 99.0011 VQMMIMIKFM 101000000.0 96.6 1000000.0 1000000.0 1369.t00001 Chromosome11 62 99.0012MMIMIKFMGV 10 1000000.0 47.1 1000000.0 1000000.0 1369.t00001Chromosome11 9 99.0067 KlYKIIIWI 9 56576.0 72.2 1000000.0 1000000.01369.t00001 Chromosome11 23 99.0068 YMIKKLLKI 9 4324.7 52.7 1000000.0788.9 1369.t10001 Chromosome11 42 99.0069 LMTLYQIQV 9 32880.1 41.71000000.0 1000000.0 1369.100001 Chromosome11 68 99.0070 FMGVIYIMI 910136.0 91.9 1000000.0 58.6 1369.t00001 Chromosome11 280 99.0071NILIVLYYL 9 117610.0 42.8 1000000.0 1000000.0 1369.t00001 Chromosome11312 99.0072 FMNRFYITT 9 14073.8 47.8 1000000.0 1000000.0 699.t00001Chromosome11 488 99.0013 YLYISFLLLI 10 311433.0 34.2 1000000.0 1000000.0699.t00001 Chromosome11 1025 99.0014 YIYIFIYLFI 10 1000000.0 19.81000000.0 1000000.0 699.t00001 Chromosome11 408 99.0073 LLDDYHFET 95923.7 39.5 1000000.0 1000000.0 699.t00001 Chromosome11 488 99.0074YIYISFLLL 9 2547.9 11.2 1000000.0 1000000.0 699.t00001 Chromosome11 57299.0075 FLTLTVYPI 9 22535.9 28.3 1000000.0 1000000.0 699.t00001Chromosome11 651 99.0076 FHEILELL 9 15575.2 47.0 1000000.0 1000000.0699.t00001 Chromosome11 782 99.0077 LLYNIIITSI 9 62668.0 50.4 1000000.01000000.0 699.t00001 Chromosome11 882 99.0078 YMNFLKFTV 9 14215.9 50.31000000.0 1000000.0 699.t00001 Chromosome11 1033 99.0079 FIYIWLHLI 96243.9 15.6 1000000.0 1000000.0 699.t00001 Chromosome11 1039 99.0080HLIIIFIFV 9 6908.2 11.5 1000000.0 1000000.0 M13Hg2.q1t3 576 99.0015FLMWSSQIII 10 96042.7 91.8 1000000.0 I000000.0 M13Hg2.q1t3 96 99.0081ILLSRFIFI 9 11278.3 22.9 1000000.0 1000000.0 M13Hg2.q1t3 508 99.0082YLNFQDNYL 9 34942.8 80.6 1000000.0 1000000.0 M13Hg2.q1t3 551 99.0083NIPYFNFFV 9 86593.7 41.8 1000000.0 1000000 0 M13Hg2.q1t3 558 99.0084FVNYFEAVV 9 15474.4 100.0 1000000.0 1000000.0 M13Hg2.q1t3 569 99.0085NIHCYTYFL 9 27934.2 25.6 1000000.0 1000000.0 M13Hg2.q1t3 576 99.0086FLMWSSQII 9 5275.5 31.9 1000000.0 1000000.0 M13Hg2.q1t3 577 99.0087LMWSSQIII 9 15320.6 46.4 1000000.0 614.0 M13Hg2.q1t3 723 99.0088ILNKISSFV 9 17591.1 89.9 1000000.0 1000000.0 Mal_5L10c4.q1t6 334 99.0089FVFFIIKNV 9 13366.7 53.5 1000000.0 1000000.0 Mal_5L10c4.q1t6 366 99.0090IQICKLYHV 9 8534.4 35.2 1000000.0 1000000.0 Mal_5L10c4.q1t6 534 99.0091YISSVNYFL 9 25585.7 24.2 1000000.0 1000000.0 Mal_5L10c4.q1t6 120599.0092 YLFQLVQSL 9 4424.1 26.3 1000000.0 1000000.0 Mal_5L10c4.q1t6 124099.0093 SIYFYWFLL 9 13813.9 27.2 1000000.0 1000000.0 Mal_5L10c4.q1t61260 99.0094 YLHIHKLFI 9 46175.4 47.6 1000000.0 1000000.0Mal_5L10c4.q1t6 1596 99.0095 ILDDSINFV 9 8148.9 41.5 1000000.0 1000000.0Mal_5L10c4.q1t6 1629 99.0096 FLPEQSYVL 9 36294.8 55.0 1000000.01000000.0 Mal_5L10c4.q1t6 1890 99.0097 ITLVIQIIYV 9 52344.4 36.61000000.0 1000000.0 Mal_5L10c4.q1t6 2106 99.0098 FLSVINASV 9 15607.817.1 1000000.0 1000000.0 571.t00003 Chromosome11 105 99.0016 ILYPSLMPYV10 1000000.0 81.0 1000000.0 1000000.0 571.t00003 Chromosome11 244399.0017 YLFGKVKFYI 10 821413.1 47.5 1000000.0 1000000.0 571.t00003Chromosome11 68 99.0099 KLINTNFYI 9 109718.5 49.2 1000000.0 1000000.0571.t00003 Chromosome11 92 99.0100 KTFIYSNFL 9 34260.6 95.5 1000000.01000000.0 571.t00003 Chromosome11 109 99.0101 SLMPYVECI 9 3307.6 80.41000000.0 1000000.0 571.t00003 Chromosome11 163 99.0102 YTNYYQSFI 914053.9 63.6 1000000.0 1000000.0 571.t00003 Chromosome11 1224 99.0103FQWEKSNKI 9 17731.1 88.1 1000000.0 1000000.0 571.t00003 Chromosome111330 99.0104 FLIKLNNE1 9 32980.5 73.6 1000000.0 1000000.0 571.t00003Chromosome11 1478 99.0105 YMYTNYLNM 9 5105.1 65.8 1000000.0 4545.4571.t00003 Chromosome11 2286 99.0106 FQGEYVSNL 9 28240.4 61.4 1000000.01000000.0 MP03072 PFC0450w 7 CAA15614 99.0018 ILILIDAASV 10 1000000.088.5 1000000.0 1000000.0 MP03072 PFC0450w 19 CAA15614 99.0019 LLITFLMINL10 1000000.0 82.3 1000000.0 1000000.0 MP03072 PFC0450w 46 CAA1561499.0020 ALVVAIILYV 10 599232.7 38.0 1000000.0 1000000.0 MP03072 PFC0450w50 CAA15614 99.0021 ATILYVIFLV 10 1000000.0 58.1 1000000.0 1000000.0MP03072 PFC0450w 52 CAA15614 99.0022 ILYVIFLVLL 10 1000000.0 33.81000000.0 1000000.0 MP03072 PFC0450w 54 CAA15614 99.0023 YVIFLVLLFI 10656413.8 20.3 1000000.0 1000000.0 MP03072 PFC0450w 57 CAA15614 99.0024FLVLLFIYKA 10 139.6 80.7 498.9 1000000.0 MP03072 PFC0450w 18 CAA1561499.0107 FLLITFLMI 9 5377.9 28.0 1000000.0 1000000.0 MP03072 PFC0450w 47CAA15614 99.0108 LVVAIILYV 9 17753.4 20.8 1000000.0 1000000.0 MP03072PFC0450w 50 CAA15614 99.0109 AIILYVIFL 9 35558.1 23.3 1000000.01000000.0 MP03072 PFC0450w 51 CAA15614 99.0110 IILYVIFLV 9 29081.2 23.41000000.0 1000000.0 MP03072 PFC0450w 52 CAA15614 99.0111 ILYVIFLVL 94626.7 49.4 1000000.0 1000000.0 MP03072 PFC0450w 55 CAA15614 99.0112VIFLVLLFT 9 17063.1 28.6 1000000 0 1000000.0 45.t00001 Chromosome14 2299.0113 YQDPQNYEL 9 17446.7 62.2 1000000.0 1000000.0 45.t00001Chromosome14 134 99.0114 KTWKPTIFL 9 18939.7 82.8 1000000.0 1000000.045.t00001 Chromosome14 142 99.0115 LLNESNIFL 9 13381.3 66.8 1000000.01000000.0 45.t00001 Chromosome14 220 99.0116 FIHFFTWGT 9 54429.1 69.21000000.0 1000000.0 MP03137 PFC0700c 180 CAB11150 99.0117 VLFLQMMNV 971815.8 72.3 1000000.0 1000000.0 MP03137 PFC0700c 251 CAB11150 99.0118NQMIFVSSI 9 39082.0 99.1 1000000.0 1000000.0 MP03137 PFC0700c 253CAB11150 99.0119 MIFVSSIFI 9 17820.1 95.9 1000000.0 1000000.0 MP03137PFC0700c 258 CAB11150 99.0120 SIFISFYLI 9 13357.1 72.3 1000000.01000000.0 MP03137 PFC0700c 293 CAB11150 99.0121 RLFEESLGI 9 22704.6 90.41000000.0 1000000.0 12.t00018 Chromosome14 870 99.0025 YLCLYNGLLL 10294216.7 79.1 1000000.0 1000000.0 12.t00018 Chromosome14 1018 99.0026YLLFFREKFL 10 1000000.0 57.8 1000000.0 1000000.0 12.t00018 Chromosome14597 99.0122 KLIEYFLNM 9 8556.1 30.0 1000000.0 1000000.0 12.t00018Chromosome14 615 99 0123 YVSMYIPFI 9 7367.7 57.9 1000000.0 1000000.012.t00018 Chromosome14 870 99.0124 YLCLYNGLL 9 12899.1 68.8 1000000.01000000.0 12.t00018 Chromosome14 893 99.0125 NIISSIFYI 9 94922.9 77.91000000.0 1000000.0 12.t00018 Chromosome14 907 99.0126 YLYDNYSHL 911094.9 55.2 1000000 0 1000000.0 12.t00018 Chromosome14 953 99.0127FLNVYENFL 9 23398.0 34.3 1000000.0 1000000.0 12.t00018 Chromosome14 103799.0128 LIFGYNSLI 9 26493.2 50.1 1000000.0 1000000.0 12.t00018Chromosome14 1047 99.0129 FLEYOCREV 9 24096.2 30.4 1000000.0 1000000.0mal_BU12129.q1c1 90 99.0130 YIYIYIYFL 9 32096.6 3.8 1000000.0 1000000.0mal_BU121g9.q1c1 92 99.0131 YIYINFLQI 9 15022.6 13.6 1000000.0 1000000.0mal_9A57b11.q1t2 138 99.0132 KQYTDIPSL 9 184531.0 81.9 1000000.01000000.0 mal_9A57h11.q1t2 158 99.0133 KVFCYEYFI 9 10650.1 18.01000000.0 1000000.0 mal_9A57611.q1t2 165 99.0134 FIFDIFKYA 9 21.1 20.244.0 1000000.0 mal_BL50e8.p1ca_5 6 99.0027 ALLSFLVVLV 10 1000000.0 42.51000000.0 1000000.0 mal_BL50c8.p1ca_5 65 99.0028 RQINFMETFV 10 1000000.054.6 1000000.0 1000000.0 mal_BL50c8.p1ca_5 4 99.0135 FVALLSFLV 9 3130.026.0 1000000.0 1000000.0 mal_BL50e8.p1ca_5 7 99.0136 LLSFLVVLV 9 11579.536.2 1000000.0 1000000.0 mal_BL50e8.p1ca_5 192 99.0137 FIYNWVLQT 930528.1 55.9 1000000.0 1000000.0 mal_BL50e8.p1ca_5 349 99.0138 ILIRALLSL9 8963.2 44.4 1000000.0 1000000.0 mal_BL50e8.p1ca_5 353 99.0139ALLSLDFSL 9 22110.4 36.6 1000000.0 1000000.0 mal_BL50e8.p1ca_5 56299.0140 NLFGGGFYI 9 22065.3 23.4 1000000.0 1000000.0 mal_BL50e8.p1ca_5779 99.0141 LMLKADYFT 9 22456.0 21.9 1000000.0 444.0 mal_BL50e8.p1ca_5973 99.0142 NIYTHSVYV 9 245555.5 53.7 1000000.0 1000000.0 M13S8h6.p1t_37 99.0143 FVLACVLLI 9 10293.7 14.2 1000000.0 1000000.0 M13S8h6.p1t_3 2399.0144 ATSTEFFFL 9 3703.8 20.0 1000000.0 1000000.0 M13S8h6.p1t_3 3499.0145 FLLICGFCI 9 23058.3 21.3 1000000.0 1000000.0 M13S8h6.p1t_3 5599.0146 VLITYSFTV 9 35516.3 7.8 1000000.0 1000000.0 M13S8h6.p1t_3 6199.0147 FIVSYIFFM 9 18627.5 9.0 1000000.0 1000000.0 M13S8h6.p1t_3 7799.0148 LLVCISILL 9 4378.4 24.2 1000000.0 1000000.0 M13S8h6.p1t_3 144799.0149 FIITYIWII 9 50315.1 20.9 1000000.0 1000000.0 M13S8h6.p1t_3 146999.0150 KMMWTIFIL 9 13621.2 14.7 1000000.0 35.6 M13S8h6.p1t_3 153899.0151 FVFFYIFLI 9 5681.7 3.2 1000000.0 1000000.0 M13S8h6.p1t_3 158299.0152 YLDRIQFLV 9 3212.4 6.0 1000000.0 1000000.0 585.t00002Chromosome11 651 99.0029 VLSPFSLIFV 10 236320.1 33.8 1000000.0 1000000.0585.t00002 Chromosome11 1380 99.0030 TLVNILILFL 10 1000000.0 25.51000000.0 1000000.0 585.t00002 Chromosome11 1406 99.0031 FVFFRFLFFV 10132657.2 16.7 1000000.0 1000000.0 585.t00002 Chromosome11 6 99.0153FILFYFYVM 9 18702.2 16.8 1000000.0 1000000.0 585.t00002 Chromosome11 1799.0154 YTFCFLPVL 9 3159.4 24.6 1000000.0 1000000.0 585.t00002Chromosome11 643 99.0155 WLFFFDLVV 9 13858.2 39.1 1000000.0 1000000.0585.t00002 Chromosome11 661 99.0156 FILFFCIFFI 9 13336.6 6.4 1000000.01000000.0 585.t00002 Chromosome11 1386 99.0157 ILFLICYSI 9 18185.7 17.81000000.0 1000000.0 585.t00002 Chromosome11 1399 99.0158 YMFSYIPFV 920964.1 1.1 1000000.0 1000000.0 585.t00002 Chromosome11 1507 99.0159YILFILFFI 9 12765.9 4.2 1000000.0 1000000.0 1223.t00015 mal_9A21f9.q1t_41387 99.0032 LIHDDVLLFL 10 1000000.0 32.2 1000000.0 1000000.01223.t00015 mal_9A2119.q1t_4 270 99.0160 FVSFYKFEV 9 10792.4 28.21000000.0 1000000.0 1223.t00015 ma1_9A2110.q1t_4 811 99.0161 MLWCSMESV 95755.3 27.5 1000000.0 1000000.0 1223.t00015 ma1_9A21f9.q1t_4 924 99.0162KLFDAINYL 9 35603.1 20.5 1000000.0 1000000.0 1223.t00015mal_9A21f9.q1t_4 1648 99.0163 FVMDITDSI 9 4215.8 44.1 1000000.01000000.0 1223.t00015 mal_9A2119.q1t_4 1853 99.0164 MLYSIVWGL 9 18338.724.8 1000000.0 1000000.0 1223.t00015 mal_9A21f9.q1t_4 2301 99.0165NIYFSYFYV 9 68948.8 41.1 1000000.0 1000000.0 1223.t00015mal_9A21f9.q1t_4 2548 99.0166 FILEHVNSI 9 80628.8 42.2 1000000.01000000.0 1223.t00015 mal_9A21f9.q1t_4 3057 99.0167 SLLKAQLFV 9 12372.415.7 1000000.0 1000000.0 1223.t00015 mal_9A21f9.q1t_4 4419 99.0168SLDEVVLYT 9 8137.8 46.3 1000000.0 1000000.0 599.t00001 Chromosome11 106999.0033 HLMHIINVFI 10 1000000.0 56.9 1000000.0 1000000.0 599.t00001Chromosome11 1341 99.0034 FLSDYTTCSV 10 93945.4 72.2 1000000.0 1000000.0599.t00001 Chromosome11 1458 99.0035 FLRNYVVIFI 10 615882.5 83.61000000.0 1000000.0 599.t00001 Chromosome11 9 99.0169 YLTINFFIL 9 4373.864.1 1000000.0 1000000.0 599.t00001 Chromosome11 883 99.0170 NMNDIENFV 932886.3 78.0 1000000.0 1000000.0 599.t00001 Chromosome11 1013 99.0171FIHDILLDL 9 11903.4 46.8 1000000 0 1000000.0 599.t00001 Chromosome111034 99.0172 NQYAYDLKI 9 38604.8 81.2 1000000.0 1000000.0 599.t00001Chromosome11 1718 99.0173 GLGGLLFII 9 5216.8 74.2 1000000.0 1000000.0599.t00001 Chromosome11 1770 99.0174 YIMNNTIFT 9 4444.5 75.2 1000000.01000000.0 599.t00001 Chromosome11 1914 99.0175 HLFNFSNFV 9 16629.7 25.51000000.0 1000000.0 MP01072 M1045c5.p1c.C_6 1138 99.0036 YLIRNILMSI 10819635.3 75.5 1000000.0 1000000.0 MP01072 M1045c5.p1c.C_6 66 99.0176YLYKSIFKA 9 6.2 29.5 1755.3 1000000.0 MP01072 M1045c5.p1c.C_6 82 99.0177YLDFYEFCV 9 5138.7 6.7 1000000.0 1000000.0 MP01072 M1045c5.p1c.C_6 116199.0178 KIPPLFFSI 9 19713.1 22.7 1000000.0 1000000.0 MP01072M1045c5.p1c.C_6 1281 99.0179 KLNEINILL 9 15599.8 69.4 1000000.01000000.0 PIR2 T28161 577 99.0037 FLMFWVAHM 10 60152.9 33.4 1000000.01000000.0 PIR2 T28161 142 99.0180 LLAEVCYAA 9 9.8 35.1 4774.0 1000000.0PIR2 T28161 369 99.0181 CLYVCDPYV 9 78244.5 58.0 1000000.0 1000000.0PIR2 T28161 577 99.0182 FLMFWVAIIM 9 3061.0 5.7 1000000.0 1000000.0 PIR2128161 642 99.0183 FQGWGHYFV 9 53546.0 13.8 1000000.0 1000000.0 PIR2128161 888 99.0184 FLGDVLFAA 9 6.7 8.3 2549.7 1000000.0 PIR2 T28161 89299.0185 VLFAANYEA 9 25.8 20.9 100.0 1000000.0 PIR2 T28161 1098 99.0186YLQAQTTAA 9 26.9 64.0 17290.2 1000000.0 PIR2 T28161 1461 99.0187FLRQMFYTL 9 8779.8 60.8 1000000.0 1000000.0 PIR2 T28161 2149 99.0188FAAFTYFYL 9 11639.0 45.5 1000000.0 1000000.0 55.t00004 Chromosome14 135899.0038 FMDSQNGMYI 10 26503.4 87.2 1000000.0 4109.6 55.t00004Chromosome14 1542 99.0039 SLINYNKYFV 10 1000000.0 43.5 1000000.01000000.0 55.t00004 Chromosome14 84 99.0189 FVVAQLYEL 9 27995.5 19.71000000.0 1000000.0 55.t00004 Chromosome14 480 99.0190 KTFFFFSNV 910931.8 72.4 1000000.0 1000000.0 55.t00004 Chromosome14 1098 99.0191IINSDDYFV 9 58940.8 86.9 1000000.0 1000000.0 55.t00004 Chromosome14 136499.0192 GMYILPQYV 9 18255.9 74.7 1000000.0 1000000.0 674.t00001Chromosome11 89 99.0040 ELVEFIFLLL 10 1000000.0 97.4 1000000.0 1000000.0674.t00001 Chromosome11 281 99.0041 FLYKDVLMDI 10 358012.1 50.41000000.0 1000000.0 674.t00001 Chromosome11 89 99.0193 ELVEFIFLL 921772.0 47.1 1000000.0 1000000.0 674.t00001 Chromosome11 1102 99.0194YLNKANPNI 9 12319.8 91.3 1000000.0 1000000.0 674.t00001 Chromosome111353 99.0195 FLQYRIPHM 9 33178.8 81.0 1000000.0 1000000.0 674.t00001Chromosome11 1430 99.0196 YIVDIFCKI 9 11720.4 48.5 1000000.0 1000000.0

TABLE 5Pf-derived A3, 11 supertype peptides scoring positive on PIC algorithmPIC Malaria locus Addn Source info Position Accession No. Peptide No.Sequence AA A*0101 A*0201 PIC A*1101 PIC A*2402 331.t00003 Chromosome10354 99.0197 KFEPFIIHVK 10 1000000.0 1000000.0 26.5 1000000.0 331.t00003Chromosome10 5 99.0294 KTMDTFYKK 9 2654.1 1000000.0 0.4 1000000.0331.t00003 Chromosome10 208 99.0295 SFFDVSKKK 9 130857.6 1000000.0 16.41000000.0 331.t00003 Chromosome10 435 99.0296 LSQLVHFYK 9 29656.21000000.0 0.6 1000000.0 331.t00003 Chromosome10 779 99.0297 SVFVRRYIK 918991.0 1000000.0 0.7 1000000.0 331.t00003 Chromosome10 988 99.0298FTFQNMYVR 9 5834.2 1000000.0 22.0 1000000.0 331.t00003 Chromosome10 132499.0299 SQNSNTFLK 9 10099.5 1000000.0 0.4 1000000.0 331.t00003Chromosome10 1337 99.0300 ILFHKFLNK 9 3064.6 1000000.0 2.4 1000000.0331.t00003 Chromosome10 1521 99.0301 NLFDENFCR 9 30418.9 1000000.0 165.91000000.0 331.t00003 Chromosome10 1551 99.0302 ALYEKVHGK 9 9346.61000000.0 4.4 1000000.0 18.000811 Chr12Contig18 17 99.0198 FLLYILFLVK 101000000 0 1000000.0 82.1 1000000.0 18.000811 Chr12Contig18 43 99.0199LVFSNVLCFR 10 365585.5 1000000.0 14.5 1000000.0 18.000811 Chr12Contig1880 99.0200 AFLESQSMNK 10 1000000.0 1000000.0 65.8 1000000.0 18.000811Chr12Contig18 112 99.0201 TFLESSFDIK 10 1000000.0 1000000.0 323.91000000.0 18.000811 Chr12Contig18 116 99.0202 SSFDIKSEVK 10 1000000.01000000.0 34.1 1000000.0 18.000811 Chr12Contig18 18 99.0303 LLYILFLVK 95498.6 1000000.0 10.1 1000000.0 18.000811 Chr12Contin18 129 99.0304KSMLKELIK 9 5942.8 1000000.0 12.7 1000000.0 18.000811 Chr12Contig18 16699.0305 PVLTSLFNK 9 10202.9 1000000.0 10.1 1000000.0 MY924Fe3.p1t1 126299.0203 TFICYYVMDK 10 1000000.0 1000000.0 23.0 1000000.0 MY924Fe3.p1t1155 99.0306 NVFNIFFEK 9 10371.8 1000000.0 0.2 1000000.0 MY924Fe3.p1t1220 99.0307 SSFLYAFNK 9 12434.3 1000000.0 0.1 1000000.0 MY924Fe3.p1t11030 99.0308 MFHIIMYTK 9 208352.1 1000000.0 18.2 1000000.0 MY924Fe3.p1t11181 99.0309 SLDDIYKYK 9 22644.9 1000000.0 2.9 1000000.0 MY924Fe3.p1t11613 99.0310 KVVVKNLYK 9 34654.1 1000000.0 0.9 1000000.0 MY924Fe3.p1t11853 99.0311 SLFRLGFVK 9 10283.0 1000000.0 0.2 1000000.0 MY924Fe3.p1t12012 99.0312 SLFFNSLYY 9 4.6 1000000.0 2.6 1000000.0 MY924Fe3.p1t1 223899.0313 ITFEKNYYR 9 21591.6 1000000.0 1.5 1000000.0 MY924Fe3.p1t1 228599.0314 SQYEENKSK 9 139775.3 1000000.0 39.1 1000000.0 MP03001 MAL3P2.1157 CAB38998 99.0204 KQENWYSLKK 10 1000000.0 1000000.0 50.6 1000000.0MP03001 MAL3P2.11 335 CAB38998 99.0205 VTCGNGIQVR 10 1000000.0 1000000.0170.6 1000000.0 MP03001 MAL3P2.11 17 CAB38998 99.0315 ALFQEYQCY 9 3.41000000.0 72.7 1000000.0 MP03001 MAL3P2.11 57 CAB38998 99.0316 KQENWYSLK9 44996.2 1000000.0 173.7 1000000.0 1369.t00001 Chromosome11 44 99.0206TLYQIQVMKR 10 1000000.0 1000000.0 52.0 1000000.0 1369.t00001Chromosome11 58 99.0207 KQVQMMIMIK 10 1000000.0 1000000.0 8.7 1000000.01369.t00001 Chromosome11 70 99.0208 GVIYIMIISK 10 1000000.0 1000000.010.6 1000000.0 1369.t00001 Chromosome11 158 99.0209 ELFDKDTFFK 101000000.0 1000000.0 14.2 1000000.0 1369.t00001 Chromosome11 18 99.0317KTMNNYMIK 9 16730.1 1000000.0 1.1 1000000.0 1369.t00001 Chromosome11 15999.0318 LFDKDTFFK 9 32977.1 1000000.0 126.3 1000000.0 1369.t00001Chromosome11 287 99.0319 YLFNQHIKK 9 21347.4 1000000.0 8.2 1000000.01369.t00001 Chromosome11 307 99.0320 MQSSFEVINR 9 12685.3 1000000.0 25.41000000.0 1369.t00001 Chromosome11 315 99.0321 RFYITTRYK 9 258367.41000000.0 21.4 1000000.0 1369.t00001 Chromosome11 319 99.0322 TTRYKYLNK9 10429.2 1000000.0 4.5 1000000.0 699.t00001 Chromosome11 464 99.0210KVCELLGYYK 10 1000000.0 1000000.0 1.1 1000000.0 699.t00001 Chromosome11492 99.0211 SFLLLIVFSK 10 1000000.0 1000000.0 21.9 1000000.0 699.t00001Chromosome11 623 99.0212 KLLYKMNYLK 10 1000000.0 1000000.0 15.01000000.0 699.t00001 Chromosome11 764 99.0213 TLEYNPSFFY 10 91.91000000.0 219.0 1000000.0 699.t00001 Chromosome11 782 99.0214 LLYNHITSIK10 1000000.0 1000000.0 12.1 1000000.0 699.t00001 Chromosome11 87899.0215 LFYLYMNFLK 10 1000000.0 1000000.0 8.2 1000000.0 699.100001Chromosome11 386 99.0323 KQNIPIYIY 9 57.8 1000000.0 175.4 1000000.0699.100001 Chromosome11 507 99.0324 KTNIFFKKK 9 23058.6 1000000.0 1.51000000.0 699.t00001 Chromosome11 734 99.0325 1VNDLGIFY 9 2.4 1000000.016.6 1000000.0 699.t00001 Chromosome11 769 99.0326 PSFFYLSFK 9 22074.61000000.0 20.1 1000000.0 mal4T2c4.p1t1 15 99.0216 ILLIRPMLVK 101000000.0 1000000.0 95.1 1000000.0 mal442c4.p1t1 29 99.0217 LVKLRPMLVK10 1000000.0 1000000.0 22.3 1000000.0 mal4T2c4.p1t1 36 99.0218LVKLGPILVK 10 1000000.0 1000000.0 15.0 1000000.0 mal4T2c4.p1t1 1699.0327 LLIRPMLVK 9 29115.0 1000000.0 16.1 1000000.0 M13Hg2.q1t3 9799.0219 LLSRFIFIYK 10 1000000.0 1000000.0 12.9 1000000.0 M13Hg2.q1t3 26799.0220 KTSDAKLVDK 10 543207.5 1000000.0 21.8 1000000.0 M13Hg2.q1t3 27799.0221 ETSTISTFIK 10 714638.7 1000000.0 21.8 1000000.0 M13Hg2.q1t3 40699.0222 IFFSYNPFHK 10 1000000.0 1000000 0 18.5 1000000.0 M13Hg2.q1t3 52899.0223 YFFNCIQMAK 10 1000000.0 1000000.0 48.6 1000000.0 M13Hg2.q1t3 999.0328 SLYNKIEYR 9 32837.9 1000000.0 36.8 1000000.0 M13Hg2.q1t3 4899.0329 SASESNFYK 9 17208.3 1000000.0 0.2 1000000.0 M13Hg2.q113 21699.0330 ISYIFPLFK 9 12671.6 1000000.0 2.2 1000000.0 M13Hg2.q1t3 42099.0331 SQNYENINK 9 36248.0 1000000.0 3.6 1000000.0 M13Hg2.q1t3 66199.0332 SLMDASKNK 9 5327.4 1000000.0 3.2 1000000.0 Mal_5L10c4.q1t6 2199.0333 KLGFFVCYK 9 42997.2 1000000.0 3.5 1000000.0 Mal_5L10c4.q1t6 3699.0334 SFKNKILQK 9 139254.7 1000000.0 14.9 1000000.0 Mal_5L10c4.q1t6 5699.0335 KFMYLRKKK 9 74875.0 1000000.0 33.4 1000000.0 Mal_5L10c4.q1t6 38199.0336 KQIIFEALK 9 120283.5 1000000.0 38.9 1000000.0 Mal_5L10c4.q1t6519 99.0337 ETFYKELYK 9 14646.9 1000000.0 1.2 1000000.0 Mal_5L10c4.q1t6537 99.0338 SVNYFLLER 9 4574.8 1000000.0 0.4 1000000.0 Mal_5L10c4.q1t6724 99.0339 ILNFLNFNK 9 12039.7 1000000.0 2.7 1000000.0 Mal_5L10c4.q1t6897 99.0340 NTCSKEIYK 9 26259.6 1000000.0 4.6 1000000.0 Mal_5110c4.q1t61316 99.0341 KLRNFLFYY 9 34.8 1000000.0 27.7 1000000.0 Mal_5L10c4.q1t61722 99.0342 CSNNNIFYK 9 16887.2 1000000.0 2.7 1000000 0 571.t00003Chromosome11 1059 99.0224 MQYNHDNIYK 10 1000000.0 1000000.0 6.81000000.0 571.t00003 Chromosome11 2438 99.0225 SFSMLYLFGK 10 1000000.01000000.0 20.1 1000000.0 571.t00003 Chromosome11 675 99.0343 ALNPKYQNH 94302.1 1000000.0 149.6 1000000.0 571.t00003 Chromosome11 749 99.0344TLNSFQHNK 9 9140.5 1000000.0 4.0 1000000.0 571.t00003 Chromosome11 122099.0345 KINEFQWEK 9 55899.8 1000000.0 0.3 1000000.0 571.t00003Chromosome11 1368 99.0346 RSDYFHNTK 9 15625.8 1000000.0 5.2 1000000.0571.t00003 Chromosome11 1429 99.0347 STNSQQLIK 9 14992.1 1000000.0 1.11000000.0 571.t00003 Chromosome11 1552 99.0348 KFMTPTTLK 9 54389.61000000.0 8.1 1000000.0 571.t00003 Cluomosome11 1684 99.0349 TTNSTPHFK 95905.8 1000000.0 3.8 1000000.0 571.t00003 Chromosome11 2509 99.0350KLMETRFSK 9 8313.3 1000000.0 2.8 1000000.0 MP03072 PFC0450w 36 CAA1561499.0226 SQAHRENGKK 10 1000000.0 1000000.0 109.2 1000000.0 MP03072PFC0450w 45 CAA15614 99.0227 KALVVAIILY 10 220.1 1000000.0 237.11000000.0 MP03072 PFC0450w 55 CAA15614 99.0228 VIFLVLLFIY 10 137.21000000.0 61.8 1000000.0 MP03072 PFC0450w 56 CAA15614 99.0229 IFLVLLFIYK10 1000000.0 1000000.0 44.3 1000000.0 MP03072 PFC0450w 58 CAA1561499.0230 LVLLFIYKAY 10 371.7 1000000.0 207.5 1000000.0 MP03072 PFC0450w59 CAA15614 99.0231 VLLFIYKAYK 10 1000000.0 1000000.0 31.2 1000000.0MP03072 PFC0450w 61 CAA15614 99.0232 LFIYKAYKNK 10 1000000.0 1000000.0434.4 1000000.0 MP03072 PFC0450w 72 CAA15614 99.0233 KLYTNFFMKK 101000000.0 1000000.0 5.8 1000000.0 MP03072 PFC0450w 92 CAA15614 99.0234STYLSASDEY 10 57.2 1000000.0 85.1 1000000.0 MP03072 PFC0450w 36 CAA1561499.0351 SQAHRENGK 9 65339.9 1000000.0 230.0 1000000.0 MP03072 PFC0450w46 CAA15614 99.0352 ALVVAIILY 9 6.0 1000000.0 95.4 1000000.0 MP03072PFC0450w 57 CAA15614 99.0353 FLVLLFIYK 9 14940.5 1000000.0 5.0 1000000.0MP03072 PFC0450w 58 CAA15614 99.0354 LVLLFIYKA 9 13.1 102.2 132.51000000.0 MP03072 PFC0450w 60 CAA15614 99.0355 LLFIYKAYK 9 59055.31000000.0 9.6 1000000.0 MP03072 PFC0450w 62 CAA15614 99.0356 FTYKAYKNK 935013.8 1000000.0 22.0 1000000.0 MP03072 PFC0450w 72 CAA15614 99.0357KLYTNFFMK 9 7491.5 1000000.0 2.3 1000000.0 MP03072 PFC0450w 74 CAA1561499.0358 YTNFFM KKR 9 18478.3 1000000.0 48.4 1000000.0 45.t00001Chromosome14 50 99.0235 ALERLLSLKK 10 1000000.0 1000000.0 149.51000000.0 45.t00001 Chromosome14 109 99.0236 KILIKIPVTK 10 1000000.01000000.0 30.2 1000000.0 45.t00001 Chromosome14 128 99.0237 RLPLLPKTWK10 1000000.0 1000000.0 19.6 1000000.0 45.t00001 Chromosome14 147 99.0238NIFLRFIPDK 10 1000000.0 1000000.0 24.9 1000000.0 45.t00001 Chromosome14161 99.0239 SQVSNSDSYK 10 1000000.0 1000000.0 36.0 1000000.0 45.t00001Chromosome14 197 99.0240 QQNQESKIMK 10 928526.9 1000000.0 431.51000000.0 45.t00001 Chromosome14 249 99.0241 IIALLIIPPK 10 1000000.0 1000000.0 19.3 1000000.0 45.t00001 Chromosome14 374 99.0242 SQDLACIFDA10 226.7 389.1 400.3 1000000.0 45.t00001 Chromosome14 34 99.0359AVIFTPIYY 9 7.6 1000000.0 4.7 1000000.0 45.t00001 Chromosome14 5099.0360 ALER LLSLK 9 6245.7 1000000.0 55.5 1000000.0 45.t00001Chromosome14 85 99.0361 SISGKYDIK 9 29562.3 1000000.0 25.1 1000000.045.t00001 Chromosome14 101 99.0362 ILCIEGEQK 9 519431 1000000.0 162.51000000.0 45.t00001 Chromosome14 126 99.0363 EQRLPLLPK 9 66848.01000000.0 244.3 1000000.0 45.t00001 Chromosome14 148 99.0364 IFLRFIPDK 9170326.8  1000000.0 112.0 1000000.0 45.t00001 Chromosome14 250 99.0365IALLIIPPK 9 47443.5 1000000.0 25.2 1000000.0 45.t00001 Chromosome14 27099.0366 PVVCSMEYK 9 20870.3 1000000.0 23.1 1000000.0 45.t00001Chromosome14 271 99.0367 VVCSMEYKK 9 24792.5 1000000.0 8.3 1000000.045.t00001 Chromosome14 308 99.0368 FSYDLRLNK 9 5228.9 1000000.0 13.41000000.0 45.t00001 Chromosome14 323 99.0369 HLNIPIGFK 9 25082.01000000.0 98.3 1000000.0 MP03137 PFC0700c 14 CAB11150 99.0243 SSPLFNNFYK10 1000000.0 1000000.0 0.5 1000000.0 MP03137 PFC0700c 151 CAB1115099.0244 FLYLLNKKNK 10 1000000.0 1000000.0 139.2 1000000.0 MP03137PFC0700c 183 CAB11150 99.0245 LQMMNVNLQK 10 1000000.0 1000000.0 83.61000000.0 MP03137 PFC0700c 195 CAB11150 99.0246 LTNHLINTPK 10 427675.01000000.0 20.8 1000000.0 MP03137 PFC0700c 259 CAB11150 99.0247IFISFYLINK 10 1000000.0 1000000.0 102.0 1000000.0 MP03137 PFC0700c 293CAB11150 99.0248 RLFEESLGIR 10 923199.1 1000000.0 420.0 1000000.0MP03137 PFC0700c 16 CAB11150 99.0370 PLFNNFYKR 9 11760.5 1000000.0 383.01000000.0 MP03137 PFC0700c 141 CAB11150 99.0371 YQNFQNADK 9 40121.51000000.0 637.4 1000000.0 MP03137 PFC0700c 184 CAB11150 99.0372QMMNVNLQK 9 17662.1 1000000.0 1.4 1000000.0 MP03137 PFC0700c 222CAB11150 99.0373 AVSEIQNNK 9 6991.0 1000000.0 3.1 1000000.0 MP03137PFC0700c 236 CAB11150 99.0374 GTMYILLKK 9 986.2 1000000.0 0.5 1000000.0MP03137 PFC0700c 260 CAB11150 99.0375 FISFYLINK 9 7376.0 1000000.0 12.21000000.0 MP03137 PFC0700c 264 CAB11150 99.0376 YLINKHWQR 9 39562.31000000.0 41.6 1000000.0 MP03137 PFC0700c 273 CAB11150 99.0377 ALKISQLQK9 37884.8 1000000.0 5.1 1000000.0 MP03137 PFC0700c 282 CAB11150 99.0378KINSNFLLK 9 5732.3 1000000.0 1.0 1000000.0 12.t00018 Chromosome14 8999.0249 QLKHFFNSNK 10 1000000.0  1000000.0 33.5 1000000.0 12.t00018Chromosome14 615 99.0250 YVSMYIPFIK 10 301060.0 1000000.0 2.6 1000000.012.t00018 Chromosome14 671 99.0251 VLFYIYNMYH 10 900700.0 1000000.0 13.61000000.0 12.t00018 Chromosome14 705 99.0252 YTYIFFNYDK 10 742244.61000000.0 2.1 1000000.0 12.t00018 Chromosome14 1140 99.0253 SFFITYSYWK10 1000000.0  1000000.0 5.7 1000000.0 12.t00018 Chromosome14 195 99.0379STSNKH1NR 9 6609.8 1000000.0 3.8 1000000.0 12.t00018 Chromosome14 68799.0380 SQCNDYYIK 9 95255.3 1000000.0 6.3 1000000.0 12.t00018Chromosome14 896 99.0381 SSIFYIKNK 9 41588.5 1000000.0 8.4 1000000.012.t00018 Chromosome14 1020 99.0382 LFFREKFLK 9 89243.3 1000000.0 14.31000000.0 12.t00018 Chromosome14 1160 99.0383 ILDNVSFLK 9 7621.11000000.0 21.0 1000000.0 mal_BU121g9.q1c1 10 99.0254 ILVLDIPGFK 101000000.0  1000000.0 55.0 1000000.0 mal_BU121g9.q1c1 45 99.0255ETYGDSLVLH 10 453286.5 1000000.0 386.1 1000000 0 mal_BU121g9.q1c1 5999.0256 EVGYFKRIFK 10 1000000.0  1000000.0 20.4 1000000.0mal_BU121g9.q1c1 11 99.0384 LVLDIPGFK 9 13172.2 1000000.0 26.7 1000000.0mal_BU121g9.q1c1 30 99.0385 GMLTVAGPR 9 54761.5 1000000.0 326.11000000.0 mal_BU121g9.q1c1 39 99.0386 SQTELFETY 9 6.7 1000000.0 254.21000000.0 mal_BU121g9.q1c1 48 99.0387 GDSLVLIIAK 9 19504.9 1000000.0306.8 1000000.0 mal_BU121g9.q1c1 50 99.0388 SLVLHAKER 9 133501.51000000.0 487.4 1000000.0 mal_BU121g9.q1c1 60 99.0389 VGYFKRIFK 944416.3 1000000.0 27.9 1000000.0 mal_BU121g9.q1c1 86 99.0390 NIYIYIYIY 940.2 1000000.0 322.7 1000000.0 mal_BU121g9.q1c1 88 99.0391 YIYIYIYIY 916.2 1000000.0 310.0 1000000.0 mal_9A57b11.q1t2 31 99.0257 SSFNCDIANK 101000000.0  1000000.0 8.4 1000000.0 mal_9A57b11.q1t2 49 99.0258SMGVFCLKEK 10 1000000.0  1000000.0 24.6 1000000.0 mal_9A57b11.q1t2 11999.0259 HIVKNRIYNK 10 1000000.0  1000000.0 51.7 1000000.0mal_9A57b11.q1t2 128 99.0260 KLKLHKIIRK 10 1000000.0  1000000.0 64.91000000.0 mal_9A57b11.q1t2 165 99.0261 FIFDIFKYAR 10 1000000.0 1000000.0 148.8 1000000.0 mal_9A57b11.q1t2 202 99.0262 AQKALSNLHK 101000000.0 1000000.0 113.8 1000000.0 mal_9A57b11.q1t2 208 99.0263NLHKSWLQYK 10 507559.4 1000000.0 199.6 1000000.0 mal_9A57b11.q1t2 23499.0264 YLPLFLMMEH 10 1000000.0 1000000.0 147.3 1000000.0mal_9A57b11.q1t2 32 99.0392 SFNCDIANK 9 27329.1 1000000.0 35.4 1000000.0mal_9A57b11.q1t2 62 99.0393 KINKKYNKK 9 40379.4 1000000.0 56.4 1000000.0mal_9A57b11.q1t2 95 99.0394 ILNNKELFK 9 13663.7 1000000.0 29.6 1000000.0mal_9A57b11.q1t2 120 99.0395 IVKNRIYNK 9 25949.5 1000000.0 17.81000000.0 mal_9A57b11.q1t2 154 99.0396 LINSKVFCY 9 6.1 1000000.0 113.81000000.0 mal_9A57b11.q1t2 183 99.0397 RQKEFYPIK 9 127059.4 1000000.038.7 1000000.0 mal_BL50e8.p1ca_5 9 99.0265 SFLVVLVFNK 10 1000000.01000000.0 33.6 1000000.0 mal_BL50e8.p1ca_5 152 99.0266 STYMTPSAIK 101000000.0 1000000.0 2.8 1000000.0 mal_BL50e8.p1ca_5 656 99.0267KLYGEFTMNK 10 1000000.0 1000000.0 1.3 1000000.0 mal_BL50e8.p1ca_5 90799.0268 GVYYIFVYLR 10 1000000.0 1000000.0 3.7 1000000.0mal_BL50e8.p1ca_5 115 99.0398 SQYSNYFDY 9 11.0 1000000.0 15.2 1000000.0mal_BL50e8.p1ca_5 361 99.0399 LFITYFQQK 9 90294.9 1000000.0 50.91000000.0 mal_BL50e8.p1ca_5 409 99.0400 ATSWDEYPK 9 44148.4 1000000.00.8 1000000.0 mal_BL50e8.p1ca_5 752 99.0401 ASFAAHENK 9 11256.91000000.0 0.2 1000000.0 mal_BL50e8.p1ca_5 780 99.0402 MLKADYFIR 935925.9 1000000.0 61.1 1000000.0 mal_BL50e8.p1ca_5 819 99.0403 VLNPVTIPK9 14931.7 1000000.0 5.6 1000000.0 M13S8h6.p1t_3 63 99.0269 VSYIFFMSFK 101000000.0 1000000.0 0.4 1000000.0 M13S8h6.p1t_3 937 99.0270 MQKYFLHISK10 1000000.0 1000000.0 37.5 1000000.0 M13S8h6.p1t_3 25 99.0404 STFFFFLSR9 3848.4 1000000.0 0.1 1000000.0 M13S8h6.p1t_3 84 99.0405 LLLTFGVYY 922.7 1000000.0 157.5 1000000.0 M13S8h6.p1t_3 157 99.0406 KFLFRYKQK 9941796.8 1000000.0 16.1 1000000.0 M13S8h6.p1t_3 394 99.0407 KVFIKGKGK 943309.1 1000000.0 3.8 1000000.0 M13S8h6.p1t_3 1449 99.0408 ITYIWIILK 96990.4 1000000.0 1.6 1000000.0 M13S8h6.p1t_3 1534 99.0409 KFFFFVFFY 951.8 1000000.0 3.5 2.2 M13S8h6.p1t_3 1655 99.0410 KLLQKLISK 9 8661.91000000.0 53.4 1000000.0 M13S8h6.p1t_3 1703 99.0411 ILNILKLAK 9 21447.11000000.0 55.0 1000000.0 585.t00002 Chromosome11 193 99.0412 SQNNFSKIK 990378.2 1000000.0 9.1 1000000.0 585.t00002 Chromosome11 300 99.0413SSLNIYNTK 9 46908.8 1000000.0 5.2 1000000.0 585.t00002 Chromosome11 52999.0414 KLFNYKFFK 9 60297.3 1000000.0 1.0 1000000.0 585.t00002Chromosome11 572 99.0415 LTFLSNIRK 9 13099.9 1000000.0 1.3 1000000.0585.t00002 Chromosome11 616 99.0416 KFFYIFHYK 9 49030.6 1000000.0 0.21000000.0 585.t00002 Chromosome11 1415 99.0417 VTCSYFIIR 9 6831.41000000.0 16.8 1000000.0 585.t00002 Chromosome11 1487 99.0418 LTCAFKIYK9 25752.8 1000000.0 0.3 1000000.0 585.t00002 Chromosome11 1508 99.0419ILFILFFIK 9 9492.2 1000000.0 1.2 1000000.0 585.t00002 Chromosome11 154199.0420 NLYFFIHNR 9 13239.8 1000000.0 59.3 1000000.0 585.t00002Chromosome11 1742 99.0421 IFLHYYFKK 9 118461.5 1000000.0 7.6 1000000.01223.t00015 mal_9A21f9.q1t_4 4294 99.0271 QVFFLQEMER 10 544655.41000000.0 27.6 1000000.0 1223.t00015 mal_9A21f9.q1t_4 272 99.0422SFYKFEVEK 9 193104.9 1000000.0 16.1 1000000.0 1223.t00015mal_9A21f9.q1t_4 325 99.0423 KTFREHFLK 9 17344.2 1000000.0 0.0221000000.0 1223.t00015 mal_9A21f9.q1t_4 992 99.0424 VSNSSQLFK 9 13528.21000000.0 5.1 1000000.0 1223.t00015 mal_9A21f9.q1t_4 1397 99.0425SLLNDVFPK 9 67376.3 1000000.0 1.2 1000000.0 1223.t00015 mal_9A21f9.q1t_41627 99.0426 KLFIFYLDK 9 25288.3 1000000.0 0.67 1000000.0 1223.t00015mal_9A21f9.q1t_4 1664 99.0427 LLNSQIIQY 9 18.6 1000000.0 160.0 1000000.01223.t00015 mal_9A21f9.q1t_4 2115 99.0428 FQGFYFLDK 9 6204.2 1000000.044.3 1000000.0 1223.t00015 mal_9A21f9.q1t_4 2412 99.0429 NTFSFSWMK 916414.9 1000000.0 0.20 1000000.0 1223.t00015 mal_9A21f9.q1t_4 450099.0430 MFYNCPVYK 9 327575.1 1000000.0 10.3 1000000.0 599.t00001Chromosome11 723 99.0272 NLLRHATFYK 10 1000000.0 1000000.0 7.4 1000000.0599.t00001 Chromosome11 1288 99.0273 SSYGYNIYFK 10 1000000.0 1000000.00.3 1000000.0 599.t00001 Chromosome11 1451 99.0274 RTYVNEYFLR 101000000.0 1000000.0 25.4 1000000.0 599.t00001 Chromosome11 16 99.0431ILLTLVFQK 9 46527.3 1000000.0 2.9 1000000.0 599.t00001 Chromosome11 2899.0432 CQNSLNYSK 9 38238.7 1000000.0 63.2 1000000.0 599.t00001Chromosome11 211 99.0433 IVNNTELNK 9 9493.8 1000000.0 3.6 1000000.0599.t00001 Chromosome11 776 99.0434 TLFSQNLFY 9 10.5 1000000.0 75.01000000.0 599.t00001 Chromosome11 1320 99.0435 TFYESVFIR 9 63945.91000000.0 27.9 1000000.0 599.t00001 Chromosome11 1370 99.0436 YFFEEFFNK9 19717.0 1000000.0 4.6 1000000.0 599.t00001 Chromosome11 1903 99.0437TTQSNNIYK 9 20011.8 1000000.0 2.1 1000000.0 MP01072 M1045c5.p1c.C_6 145199.0275 SLFYFTSNGK 10 1000000.0 1000000.0 8.0 1000000.0 MP01072M1045c5.p1c.C_6 46 99.0438 KLNYDNFEK 9 48445.0 1000000.0 3.4 1000000.0MP01072 M1045c5.p1c.C_6 327 99.0439 ILCDDGIYR 9 19413.7 1000000.0 65.31000000.0 MP01072 M1045c5.p1c.C_6 359 99.0440 KVADVFLQII 9 6428.61000000.0 4.4 1000000.0 MP01072 M1045c5.p1c.C_6 419 99.0441 STSFLFLRK 92370.1 1000000.0 0.2 1000000.0 MP01072 M1045c5.p1c.C_6 421 99.0442SFLFLRKQK 9 408258.6 1000000.0 12.7 1000000.0 MP01072 M1045c5.p1c.C_6558 99.0443 SFFSSCENK 9 55537.2 1000000.0 17.7 1000000.0 MP01072M1045c5.p1c.C_6 609 99.0444 AQSSYIYNK 9 18056.8 1000000.0 2.5 1000000.0MP01072 M1045c5.p1c.C_6 1027 99.0445 MSAKYLYHK 9 5370.6 1000000.0 8.81000000.0 MP01072 M1045c5.p1c.C_6 1047 99.0446 TTLFSHFNK 9 10524.01000000.0 0.2 1000000.0 MP01072 M1045c5.p1c.C_6 1215 99.0447 SVYYNTMLR 99856.9 1000000.0 1.2 1000000.0 PIR2 T28161 1124 99.0276 VVNFLFELYK 10408697.6 1000000.0 3.5 1000000.0 PIR2 T28161 1403 99.0277 TFFLWDRYKK 101000000.0 1000000.0 9.0 1000000.0 PIR2 T28161 108 99.0448 SVGACAPYR 959804.6 1000000.0 2.1 1000000.0 PIR2 T28161 204 99.0449 KQLEDNLRK 987893.1 1000000.0 16.9 1000000.0 PIR2 T28161 758 99.0450 KVASNMHHK 96948.7 1000000.0 1.6 1000000.0 PIR2 T28161 760 99.0451 ASNMHHKKK 932965.2 1000000.0 4.3 1000000.0 PIR2 T28161 838 99.0452 AGFISNTYK 9154161.8 1000000.0 2.2 1000000.0 PIR2 T28161 965 99.0453 ILAFKEIYK 914274.5 1000000.0 12.6 1000000.0 PIR2 T28161 1879 99.0454 ALFKRWLEY 93.4 1000000.0 27.4 1000000.0 PIR2 T28161 2151 99.0455 AFTYFYLKK 940565.6 1000000.0 1.6 1000000.0 55.t00004 Chromosome14 483 99.0278FFFSNVNNNK 10 409139.5 1000000.0 408.4 1000000.0 55.t00004 Chromosome14564 99.0279 SQGKKNTYLK 10 1000000.0 1000000.0 13.0 1000000.0 55.100004Chromosome14 976 99.0280 VFNNSIILEK 10 1000000.0 1000000.0 372.41000000.0 55.t00004 Chromosome14 1338 99.0281 SVSEGYTSTY 10 67.81000000.0 33.5 1000000.0 55.t00004 Chromosome14 229 99.0456 TSICKYWIK 98242.3 1000000.0 14.6 1000000.0 55.t00004 Chromosome14 263 99.0457TTICKHWKK 9 4558.7 1000000.0 1.7 1000000.0 55.t00004 Chromosome14 53799.0458 KVTNVHIYK 9 41321.8 1000000.0 0.2 1000000.0 55.t00004Chromosome14 866 99.0459 ITNMNNINR 9 5371.8 1000000.0 37.6 1000000.055.t00004 Chromosome14 909 99.0460 MLNIYKINK 9 17179.3 1000000.0 13.61000000.0 55.t00004 Chromosome14 1030 99.0461 IINSYIDYK 9 84561.61000000.0 2.0 1000000.0 55.t00004 Chromosome14 1141 99.0462 NLYTYVVNK 945076.1 1000000.0 54.8 1000000.0 55.t00004 Chromosome14 1665 99.0463KMIYSIFIK 9 42191.9 1000000.0 4.1 1000000.0 13.t00011 Chromosome14 899.0282 ISMDKSLFFK 10 1000000.0 1000000.0 16.7 1000000.0 13.t00011Chromosome14 47 99.0283 TVFLDYVKGK 10 1000000.0 1000000.0 7.8 1000000.013.t00011 Chromosome14 59 99.0284 DVYKETNMNR 10 1000000.0 1000000.0 64.91000000.0 13.t00011 Chromosome14 117 99.0285 KLKKSTICNK 10 1000000.01000000.0 59.9 1000000.0 13.t00011 Chromosome14 9 99.0464 SMDKSLFFK 94208.2 1000000.0 3.5 1000000.0 13.t00011 Chromosome14 12 99.0465KSLFFKSLK 9 64105.1 1000000.0 17.4 1000000.0 13.t00011 Chromosome14 4899.0466 VFLDYVKGK 9 347222.4 1000000.0 216.7 1000000.0 13.t00011Chromosome14 93 99.0467 KVKRFRVFK 9 52490.3 1000000.0 3.3 1000000.013.t00011 Chromosome14 104 99.0468 SFFIDEVKK 9 352606.0 1000000.0 37.81000000.0 13.t00011 Chromosome14 112 99.0469 KIYENKLKK 9 30696.41000000.0 14.5 1000000.0 37.t00002 Chromosome14 13 99.0286 ALTYMYCVYY 10249.1 1000000.0 112.8 1000000.0 37.t00002 Chromosome14 31 99.0287SQISIFCNLR 10 1000000.0 1000000.0 226.6 1000000.0 37.t00002 Chromosome1432 99.0288 QISIFCNLRR 10 301919.5 1000000.0 80.8 1000000 0 37.t00002Chromosome14 62 99.0289 VCNNETYYNK 10 1000000.0 1000000.0 186.81000000.0 37.t00002 Chromosome14 71 99.0290 KAHEENDKVK 10 1000000.01000000.0 956.7 1000000.0 37.t00002 Chromosome14 13 99.0470 ALTYMYCVY 99.1 1000000.0 279.6 1000000.0 37.t00002 Chromosome14 32 99.0471QISIFCNLR 9 26897.2 1000000.0 855.0 1000000.0 37.t00002 Chromosome14 3399.0472 ISIFCNLRR 9 37287.9 1000000.0 255.9 1000000.0 37.t00002Chromosome14 61 99.0473 NVCNNETYY 9 25.3 1000000.0 514.8 1000000.0674.t00001 Chromosome11 90 99.0291 LVEFIFLLLK 10 304423.1 1000000.0 13.71000000.0 674.t00001 Chromosome11 218 99.0292 SVFYNKEIIK 10 993500.31000000.0 4.5 1000000.0 674.t00001 Chromosome11 867 99.0293 SLKDFDMLLY10 199.3 1000000.0 214.4 1000000.0 674.t00001 Chromosome11 64 99.0474NVNDRFVEK 9 13728.8 1000000.0 11.8 1000000.0 674.t00001 Chromosome11 66299.0475 TLSNSLPQK 9 36834.4 1000000.0 47.0 1000000.0 674.t00001Chromosome11 673 99.0476 YQINNFIHK 9 12103.7 1000000.0 59.8 1000000.0674.t00001 Chromosome11 689 99.0477 NLTINNFQK 9 59129.2 1000000.0 40.31000000.0 674.t00001 Chromosome11 1035 99.0478 KFNRDMLQK 9 254779.41000000.0 1.9 1000000.0 674.t00001 Chromosome11 1126 99.0479 NQSDFLLLK 98015.9 1000000.0 15.2 1000000.0 674.t00001 Chromosome11 1256 99.0480SFHHFNIDK 9 178323.3 1000000.0 26.2 1000000.0 674.t00001 Chromosome111288 99.0481 KSKELLLQK 9 27230.7 1000000.0 4.4 1000000.0

TABLE 6Pf-derived 15mer peptides with nonamer core sequences scoring DR1 PIC <4 nMAddn Peptide Antigen Source info Position No. Sequence AA DR1 PIC331.t00003 Chromosome10 182 100.0001 LSHFKKNFILQNNEE 15 0.447 331.t00003Chromosome10 365 100.0002 TTFLSALKLLKIAQY 15 0.400 331.t00003Chromosome10 428 100.0003 NNKLSKNLSQLVHFY 15 0.130 331.t00003Chromosome10 617 100.0004 KIYMFGGFSKGVRNN 15 0.061 331.t00003Chromosome10 894 100.0005 DDMIGMPNLSSTVVC 15 0.337 331.t00003Chromosome10 987 100.0006 TFTFQNMYVRSKVVS 15 0.400 331.t00003Cluumosome10 1365 100.0007 KYEIIGNILIFHYKY 15 0.435 331.t00003Chromosome10 1601 100.0008 KERMKNMYIVSNNDD 15 0.013 331.t00003Chromosome10 1656 100.0009 GVGYFTLPLLKCIEA 15 0.302 331.t00003Chromosome10 1725 100.0010 HRIILGLLPHSQPAW 15 0.167 Chr12Contig1818.000811 13 100.0011 HFFLFLLYILFLVKM 15 1.826 Chr12Contig18 18.00081116 100.0012 LFLLYILFLVKMNAL 15 0.593 Chr12Contig18 18.000811 21 100.0013ILFLVKMNALRRLPV 15 0.035 Chr12Contig18 18.000811 27 100.0014MNALRRLPVICSFLV 15 3.206 Chr12Contig18 18.000811 79 100.0015SAFLESQSMNKIGDD 15 3.392 Chr12Contig18 18.000811 132 100.0016LKELIKVGLPSFENL 15 0.785 Chr12Contig18 18.000811 143 100.0017FENLVAENVKPPKVD 15 0.854 Chr12Contig18 18.000811 148 100.0018AENVKPPKVDPATYG 15 3.392 Chr12Contia18 18.000811 158 100.0019PATYGIIVPVLTSLF 15 0.221 Chr12Contig18 18.000811 161 100.0020YGIIVPVLTSLFNKV 15 0.956 MY924Fe3.p1t1 1015 100.0021 SVDLQIKISMKVLNS 150.103 MY924Fe3.p1t1 1021 100.0022 KISMKVLNSMFHIIM 15 0.234 MY924Fc3.p1t11076 100.0023 KDVVQIQTVLLSLGT 15 0.066 MY924Fe3.p1t1 1331 100.0024SQIIIILPSILENIL 15 0.092 MY924Fc3.p1t1 1526 100.0025 MHSVKFMIVYLIQNN 150.262 MY924Fe3.p1t1 1703 100.0026 TINLINELMKRQHDK 15 0.192 MY924Fe3.p1t11746 100.0027 REMLLKMKSMSRNQR 15 0.130 MY924Fe3.p1t1 1878 100.0028RSIIFAGHTIELNSL 15 0.248 MY924Fe3.p1t1 1890 100.0029 NSLMFKQTSGRAGRR 150.061 MY924Fe3.p1t1 2201 100.0030 NLIITYLLIKKVLHN 15 0.162 MP03001MAL3P2.11 1 100.0031 MRKLAILSVSSFLFV 15 2.786 MP03001 MAL3P2.11 36100.0032 ELNYDNAGTNLYNEL 15 1.040 MP03001 MAL3P2.11 342 100.0033QVRIKPGSANKPKDE 15 0.460 1369.t00001 Chromosome11 28 100.0034LLKIWKNYMKIMNHL 15 0.328 1369.t00001 Chromosome11 43 100.0035MTLYQIQVMKRNQKQ 15 0.056 1369.t00001 Chromosome11 57 100.0036QKQVQMMIMIKFMGV 15 0.016 1369.t00001 Chromosome11 63 100.0037MIMIKFMGVIYIMII 15 0.545 1369.t00001 Chromosome11 70 100.0038GVIYIMIISKKMMRK 15 0.076 1369.t00001 Chromosome11 285 100.0039LYYLFNQHIKKEINH 15 0.742 1369.t00001 Chromosome11 299 100.0040HFNMLKNKMQSSEEM 15 0.560 1369.t00001 Chromosome11 353 100.0041XDIYQKLYIKQEEQK 15 0.807 1369.t00001 Chromosome11 366 100.0042QKKYIYNLIMNTQNK 15 0.167 1369.t00001 Chromosome11 381 100.0043YEALIKLLPFSKRIR 15 0.701 699.t00001 Chromosome11 565 100.0044NIHFAVLFLTLTVYP 15 0.347 699.t00001 Chromosome11 569 100.0045AVLFLTLTVYPINNF 15 0.255 699.t00001 Chromosome11 623 100.0046KLLYKMNYLKQDINN 15 0.545 699.t00001 Chromosome11 744 100.0047KKEFKNSLILLNLYN 15 0.576 699.t00001 Chromosome11 773 100.0048YLSFKILNTLLYNHI 15 0.234 699.t00001 Chromosome11 866 100.0049IYILINHVIIPSITY 15 0.400 699.t00001 Chromosome11 875 100.0050IPSLFYLYMNFLKFI 15 0.347 699.t00001 Chromosome11 929 100.0051KYLIILLYIFKLIEY 15 0.701 699.t00001 Chromosome11 978 100.0052FIFMQNNQTKLAEMK 15 0.039 699.t00001 Chromosome11 1032 100.0053LFIYIWLHLIIIFIF 15 0.423 mal_4T2c4.p1t1 15 100.0054 ILLIRPMLVKLRPKL 150.221 mal_4T2c4.p1t1 19 100.0055 RPMLVKLRPKLVKLR 15 0.083 mal_4T2c4.p1t126 100.0056 RPKLVKLRPMLVKLG 15 0.010 mal_4T2c4.p1t1 33 100.0057RPMLVKLGPILVKLR 15 0.004 mal_4T2c4.p1t1 40 100.0058 GPILVKLRPMLVKLR 150.010 mal_4T2c4.p1t1 47 100.0059 RPMLVKLRPMLAKLR 15 0.016 mal_4T2c4.p1t154 100.0060 RPMLAKLRPMLAKLR 15 0.027 mal_4T2c4.p1t1 61 100.0061RPMLAKLRPKLVKLR 15 0.137 mal_(—4)T2c4.p1t1 68 100.0062 RPKLVKLRPKLVKLR15 0.083 mal_4T2c4.p1t1 75 100.0063 RPKLVKLRPISVNAK 15 0.076 M13Hg2.q1t389 100.0064 ILEMKPNILLSREIF 15 0.742 M13Hg2.q1t3 122 100.0065NISINNAFSLPVNIY 15 0.663 M13Hg2.q1t3 163 100.0066 YFNIIQQKIQSNFLL 150.487 M13Hg2.q1t3 281 100.0067 ISTFIKNNINHQENN 15 0.682 M13Hg2.q1t3 442100.0068 LKNMDGNILIKDFIQ 15 0.378 M13Hg2.q1t3 488 100.0069IEFYNINMAKKVMNN 15 0.285 M13Hg2.q1t3 492 100.0070 NINMAKKVMNNMEKN 150.145 M13Hg2.q1t3 558 100.0071 FVNYFEAVVHMNIHC 15 0.831 M13Hg2.q1t3 691100.0072 NNNIINGHMLEQKLS 15 0.123 M13Hg2.q1t3 869 100.0073NNDMKKGYTNVSNNS 15 0.162 Mal_5L10c4.q1t6 154 100.0074 NNEFFGYPLQFVCET 150.255 Mal_5L10c4.q1t6 336 100.0075 FFIIKNVGVHKITYY 15 0.388Mal_5L10c4.q1t6 1090 100.0076 KIEYISMLSPTINEI 15 0.113 Mal_5L10c4.q1t61101 100.0077 INEIKTLNTILTIPL 15 0.018 Mal_5L10c4.q1t6 1107 100.0078LNTILTIPLIKMNEY 15 0.042 Mal_5L10c4.q1t6 1264 100.0079 HKLFINKLMTSNIRK15 0.203 Mal_5L10c4.q1t6 1289 100.0080 QNRERNQLLYLTKIA 15 0.050Mal_5L10c4.q1t6 1609 100.0081 IKKIKTPLILPIDPN 15 0.035 Mal_5L10c4.q1t61888 100.0082 QDHLVIQIIYVMDNI 15 0.133 Mal_5L10c4.q1t6 2031 100.0083IEAMGOAHSIGYEQF 15 0.068 571.t00003 Chromosome11 33 100.0084FDDFKINYSYKTKNH 15 0.182 571.t00003 Chromosome11 462 100.0085ITDLNNMNVNQSNMK 15 0.500 571.t00003 Chromosome11 960 100.0086TNNFNNNVMMLMNTS 15 0.007 571.t00003 Chromosome11 1124 100.0087EQNVAQNVAQNVAQN 15 0.460 571.t00003 Chromosome11 1128 100.0088AQNVAQNVAQNVEQN 15 0.460 571.t00003 Chromosome11 1550 100.0089SNKFMTPTTLKEKYQ 15 0.255 571.t00003 Chromosome11 1941 100.0090NIHMINDVATKLNQH 15 0.285 571.t00003 Chromosome11 2112 100.0091HIHMMNQQIQKETNT 15 0.576 571.t00003 Chromosome11 2255 100.0092NNVFQQPLSYSNGSE 15 0.347 571.t00003 Chromosome11 2738 100.0093NNTINMNGMNKTESI 15 0.198 MP03072 PFC0450w 5 100.0094 LNILILIDAASVAFL 150.722 MP03072 PFC0450w 8 100.0095 LILIDAASVAFLLIT 15 1.340 MP03072PFC0450w 17 100.0096 AFLLITFLMINLNEE 15 1.197 MP03072 PFC0450w 44100.0097 KKALVVAIILYVIEL 15 0.302 MP03072 PFC0450w 48 100.0098VVAIILYVIFLVLLF 15 0.609 MP03072 PFC0450w 52 100.0099 ILYVIFLVLLFIYKA 150.831 MP03072 PFC0450w 55 100.0100 VIFLVLLFIYKAYKN 15 0.956 MP03072PFC0450w 58 100.0101 LVLLFIYKAYKNKRK 15 4.016 MP03072 PFC0450w 76100.0102 NFFMKKRNAPKYVQL 15 0.593 MP03072 PEC0450w 85 100.0103PKYVQLASTYLSASD 15 2.865 45.t00001 Chromosome14 2 100.0104ENEYATGAVRPFQAA 15 0.722 45.t00001 Chromosome14 27 100.0105NYELSKKAVIFTPIY 15 1.197 45.t00001 Chromosome14 108 100.0106QKILIKIPVTKNIIT 15 0.085 45.t00001 Chromosome14 156 100.0107KCLVISQVSNSDSYK 15 2.044 45.t00001 Chromosome14 202 100.0108SKIMKLPKLPISNGK 15 0.742 45.t00001 Chromosome14 220 100.0109FIHFFTWGTMFVPKY 15 0.026 45.t00001 Chromosome14 242 100.0110LCNFKKNIIALLIIP 15 0.203 45.t00001 Chromosome14 246 100.0111KKNIIALLIIPPKIH 15 0.010 45.t00001 Chromosome14 251 100.0112ALLIIPPKIHISIEL 15 1.267 45.t00001 Chromosome14 274 100.0113SMEYKKDFLITARKP 15 1.826 MP03137 PFC0700c 7 100.0114 KSKFNILSSPLFNNF 151.987 MP03137 PFC0700c 173 100.0115 FKKLKNHVLFLQMMN 15 0.785 MP03137PFC0700c 177 100.0116 KNHVLFLQMMNVNLQ 15 0.095 MP03137 PFC0700c 180100.0117 VLFLQMMNVNLQKQL 15 0.068 MP03137 PFC0700c 187 100.0118NVNLQKQLLTNHLIN 15 0.956 MP03137 PFC0700c 191 100.0119 QKQLLTNHLINTPKI15 1.132 MP03137 PFC0700c 197 100.0120 NHLINTPKIMPHHII 15 0.576 MP03137PFC0700c 239 100.0121 YILLKKILSSRFNQM 15 1.100 MP03137 PFC0700c 250100.0122 FNQMIFVSSIFISFY 15 2.420 12.t00018 Chromosome14 36 100.0123CNILKENNTYKQKKH 15 4.016 12.t00018 Chromosome14 133 100.0124TNELKKMDTKKDVHM 15 1.011 12.t00018 Chromosome14 504 100.0125EVKFILHMTLLTLYK 15 0.269 12.t00018 Chromosome14 542 100.0126KYNFLNIYASLRNEY 15 0.328 12.t00018 Chromosome14 583 100.0127TRCFKNSYPKKVWKK 15 0.293 12.t00018 Chromosome14 612 100.0128NNLYVSMYIPFIKKF 15 0.411 12.t00018 Chromosome14 1000 100.0129EAKFKIERLLKSSYK 15 3.298 12.t00018 Chromosome14 1057 100.0130KIYILNNNLLIVHLS 15 1.543 12.t00018 Chromosome14 1184 100.0131KCSFDKTNPIQQSGK 15 2.044 12.t00018 Chromosome14 1212 100.0132TGIFNMPNLVQINNY 15 0.078 mal_BU121g9.q1c1 29 100.0133 EGMLTVAGPRSQTEL 153.298 mal_9A57b11.q1t2 3 100.0134 KQNIKYTQIISIDNI 15 2.633mal_9A57b11.q1t2 18 100.0135 LNKIADPILIGFSSS 15 0.929 mal_9A57b11.q1t2123 100.0136 NRIYNKLKLHKIIRK 15 1.267 mal_9A57b11.q1t2 194 100.0137NNEYGILNAQKALSN 15 0.098 mal_9A57b11.q1t2 197 100.0138 YGILNAQKALSNLHK15 0.141 mal_9A57b11.q1t2 229 100.0139 KIFVKYLPLFLMMEH 15 0.042mal_9A57b11.q1t2 236 100.0140 PLFLMMEHSFLNCHK 15 3.031 mal_BL50e8.p1ca_51 100.0141 MEGFVALLSFLVVLV 15 0.004 mal_BL50e8.p1ca_5 100 100.0142VDGMKIGHPISVALG 15 0.010 mal_BL50e8.p1ca_5 151 100.0143 GSTYMTPSAIKIKVP15 0.057 mal_BL50e8.p1ca_5 189 100.0144 NNLFIYNWVLQTSSP 15 0.560mal_BL50e8.p1ca_5 347 100.0145 EKILIRALLSLDFSL 15 0.722mal_BL50e8.p1ca_5 437 100.0146 HPVYPTAPAVAFPAG 15 0.187mal_BL50e8.p1ca_5 585 100.0147 EVYYFPGKVTRVRAK 15 0.357mal_BL50e8.p1ca_5 606 100.0148 EDKLVKIYISLLSSD 15 0.423mal_BL50e8.p1ca_5 685 100.0149 IERYVGLGSFHFYLY 15 0.423mal_BL50e8.p1ca_5 816 100.0150 CFQVLNPVTIPKYCI 15 0.285 M13S8h6.p1t_3 68100.0151 FMSFKILEALLVCIS 15 0.006 M13S8h6.p1t_3 127 100.0152KQIVIFLISLLSFFL 15 0.473 M13S8h6.p1t_3 169 100.0153 AKQIEILHTMLPNFL 150.095 M13S8h6.p1t_3 218 100.0154 IDDFQNMVSTLQPHV 15 0.034 M13S8h6.p1t_3285 100.0155 KCAIKLAIAQLSAKY 15 0.130 M13S8h6.p1t_3 343 100.0156IGSVKPQYALFGDTV 15 0.228 M13S8h6.p1t_3 871 100.0157 KIYIKKKRLLQMNNY 150.411 M13S8h6.p1t_3 1350 100.0158 KKLLKKLTSNLQLNK 15 0.076 M13S8h6.p1t_31602 100.0159 QDFLTKILPRQVLEF 15 0.241 M13S846.p1t_3 1754 100.0160MWGLDVLIANKIESN 15 0.423 585.t00002 Chromosome11 5 100.0161FFILFYFYVMSTYTF 15 0.500 585.t00002 Chromosome11 16 100.0162TYTFCFLPVLQTQLG 15 0.515 585.t00002 Chromosome11 349 100.0163KKKYKNKKMPKTIDG 15 0.473 585.t00002 Chromosome11 487 100.0164GRAIIPLFLILNTYK 15 0.269 585.t00002 Chromosome11 562 100.0165KIIFKRNPLFLTFLS 15 0.367 585.t00002 Chromosome11 643 100.0166WLFFFDLVVLSPFSL 15 0.500 585.t00002 Chromosome11 774 100.0167KNIIKGKNMMTRGGG 15 0.106 585.t00002 Chromosome11 796 100.0168KMFIKGDTVMKANII 15 0.038 585.t00002 Chromosome11 1093 100.0169VGSYKLMISQEAEFE 15 0.487 585.t00002 Chromosome11 1344 100.0170LNRFITLITWTQHVS 15 0.095 1223.t00015 mal9A21f9.q1t4 1070 100.0171RTKYETLVTIHVHQR 15 0.087 1223.t00015 mal9A21f9.qlt4 1162 100.0172GLCYGGAPAGPAGTG 15 0.059 1223.t00015 mal9A21f9.q1t4 1654 100.0173DSILILQTINLLNSQ 15 0.177 1223.t00015 mal9A21f9.q1t4 2461 100.0174KHLIIINRVMQTPNG 15 0.043 1223.t00015 mal9A21f9.q1t4 2779 100.0175IDLYKQMYVKKYDEI 15 0.158 1223.t00015 mal9A21f9.q1t4 2878 100.0176DKDLKAALPYLHEAE 15 0.103 1223.t00015 mal9A21f9.q1L4 2985 100.0177TIELLKPYIQSTFFK 15 0.145 1223.t00015 mal9A21f9.q1t4 2995 100.0178STFFKTQIAKKASVA 15 0.002 1223.t00015 mal9A21f9.91t44 3014 100.0179CKWVGAMAMYNQASK 15 0.145 1223.t00015 mal9A21f9.q1t4 3019 100.0180AMAMYNQASKIVKPK 15 0.116 599.t00001 Chromosome11 12 100.0181INFFILLTLVFQKYS 15 0.177 599.t00001 Chromosome11 364 100.0182NNNLGIPTLIKKEVH 15 0.234 599.t00001 Chromosome11 519 100.0183EEDIKNAYLPENKNF 15 0.435 599.t00001 Chromosome11 1074 100.0184INVFIKEISKLFDHD 15 0.529 599.t00001 Chromosome11 1414 100.0185DKSLKIMYSLFNKYT 15 0.098 599.t00001 Chromosome11 1463 100.0186VVIFIYGNIIISDLK 15 0.645 599.t00001 Chromosome11 1621 100.0187CESFISKVTNKVIKK 15 0.215 599.t00001 Chromosome11 1740 100.0188ICTFVKYITFQLLNI 15 0.854 599.t00001 Chromosome11 1767 100.0189KEHYIMNNTIFTFNQ 15 0.141 599.t00001 Chromosome11 1892 100.0190KKKYKYIPSNGTTQS 15 0.500 M1045c5.p1c.C_6 53 100.0191 EKSLGILGSIQNAYL 150.085 M1045c5.plc.C_6 59 100.0192 LGSIQNAYLYKSIFK 15 0.388M1045c5.p1c.C_6 588 100.0193 SCIMNNMIVTKESNE 15 0.473 M1045c5.p1c.C_61040 100.0194 KDFMKNNTTLFSHFN 15 0.241 M1045c5.p1c.C_6 1136 100.0195MLYLIRNILMSIEDY 15 0.435 M1045c5.p1c.C_6 1229 100.0196 KKKYIKLNIFKNIIL15 0.378 M1045c5.p1c.C_6 1350 100.0197 RWDLVMNMMIGIRIS 15 0.054M1045c5.p1c.C_6 1380 100.0198 HKDVIQLPTSNAQHK 15 0.167 M1045e5.p1c.C_61393 100.0199 HKVIFKNYAPIIFKN 15 0.262 M1045c5.p1c.C_6 1430 100.0200SNMVLGNLSTLSELL 15 0.423 PIR2 T28161 46 100.0201 AKFYNGGEIMQPNSK 150.153 PIR2 T28161 319 100.0202 KRNLKLQNAIKNCRG 15 0.043 PIR2 T28161 1072100.0203 HVKIIKNLLIHGKEQ 15 0.302 PIR2 T28161 1093 100.0204KYKLLYLQAQTTAAN 15 0.141 PIR2 T28161 1096 100.0205 LLYLQAQTTAANGGP 150.047 PIR2 T28161 1589 100.0206 SPKIVVPAPKVITTF 15 0.119 PIR2 T281611951 100.0207 FVDLIRQIAATIDKG 15 0.047 PIR2 T28161 2065 100.0208QERLVKNPLVQPTLK 15 0.028 PIR2 T28161 2129 100.0209 HPAVIPALVTSTLAW 150.072 PIR2 T28161 2419 100.0210 NELMTNHVKQTSIEI 15 0.098 55.t00004Chromosome14 81 100.0211 NNEFVVAQLYELNNY 15 1.340 55.t00004 Chromosome14117 100.0212 DNNMKKYLIQKCGKK 15 1.776 55.t00004 Chromosome14 218100.0213 SCSIIKYELRKTSIC 15 1.878 55.t00004 Chromosome14 385 100.0214RNHMDKPPPHNINNN 15 1.228 55.t00004 Chromosome14 613 100.0215NNNLIFQNSRENDHT 15 0.423 55.t00004 Chromosome14 754 100.0216THDIIKNVSNNMKRF 15 0.357 55.t00004 Chromosome14 904 100.0217FKNVDMLNIYKINKD 15 1.987 55.t00004 Chromosome14 1136 100.0218MKDVINLYTYVVNKK 15 0.092 55.t00004 Chromosome14 1364 100.0219GMYILPQYVTRECIN 15 1.500 55.t00004 Chromosome14 1510 100.0220GDDVIYEETKKTDNI 15 1.587 13.t00011 Chromosome14 16 100.0221FKSLKNNNMLESTGI 15 1.587 13.t00011 Chromosome14 49 100.0222FTDYVKGKMMDVYKE 15 0.126 13.t00011 Chromosome14 84 100.0223TYNYLTPTLKVKKEN 15 3.589 37.t00002 Chromosome14 50 100.0224NDLIDQNIVYLNVCN 15 2.560 674.t00001 Chromosome11 30 100.0225LKKLKKILLNLDVLI 15 0.742 674.t00001 Chromosome11 54 100.0226NENFDMELLNNVNDR 15 1.378 674.t00001 Chromosome11 124 100.0227NCPIKNEVTTLIQKI 15 0.367 674.t00001 Chromosome11 296 100.0228EKNMTSQKSITSEKN 15 0.854 674.t00001 Chromosome11 577 100.0229NSNFKEQHLLFCNNL 15 1.418 674.t00001 Chromosome11 752 100.0230NNNIKTHIANFNIIH 15 1.040 674.t00001 Chromosome11 986 100.0231NNLYKTYEMIQGDND 15 0.956 674.t00001 Chromosome11 1093 100.0232NDNYINNNIYLNKAN 15 1.340 674.t00001 Chromosnme11 1353 100.0233FLQYRIPHMNNNGNI 15 0.983 674.t00001 Chromosome11 1432 100.0234VDIFCKIHALKNENK 15 0.854

1. An isolated or purified polynucleotide: a) encoding a polypeptidecomprising SEQ ID NO: 2; b) encoding a Human Leukocyte Antigen (HLA)binding fragment of SEQ ID NO: 2, said fragment comprising at least fiveconsecutive amino acids of SEQ ID NO: 2; or c) that is complementaryalong the full length of said polynucleotide of a) or b).
 2. Theisolated or purified polynucleotide according to claim 1, wherein saidpolynucleotide encodes said polypeptide comprising SEQ ID NO:
 2. 3. Theisolated or purified polynucleotide according to claim 1, wherein saidpolynucleotide encodes said FILA binding fragment.
 4. The isolated orpurified polynucleotide according to claim 1, wherein saidpolynucleotide is complementary along the full length of saidpolynucleotide of a).
 5. The isolated or purified polynucleotideaccording to claim 1, wherein said polynucleotide is complementary alongthe full length of said polynucleotide of b).
 6. A vector comprising apromoter operably linked to a polynucleotide: a) encoding a polypeptidecomprising SEQ ID NO: 2; b) encoding a Human Leukocyte Antigen (HLA)binding fragment of SEQ ID NO: 2, said fragment comprising at least fiveconsecutive amino acids of SEQ ID NO: 2; or c) that is complementaryalong the full length of said polynucleotide of a) or b).
 7. The vectoraccording to claim 6, wherein said polynucleotide encodes saidpolypeptide comprising SEQ ID NO:
 2. 8. The vector according to claim 6,wherein said polynucleotide encodes said HLA biding fragment.
 9. Thevector according to claim 6, wherein said polynucleotide iscomplementary along the full length of said polynucleotide of a). 10.The vector according to claim 6, wherein said polynucleotide iscomplementary along the full length of said polynucleotide of b).
 11. Anisolated transformed host cell comprising a polynucleotide: a) encodinga polypeptide comprising SEQ ID NO: 2; b) encoding a Human LeukocyteAntigen (HLA) binding fragment of SEQ ID NO: 2, said fragment comprisingat least five consecutive amino acids of SEQ ID NO: 2; or c) that iscomplementary along the full length of said polynucleotide of a) or b).12. The isolated transformed host cell according to claim 11, whereinsaid polynucleotide encodes said polypeptide comprising SEQ ID NO: 2.13. The isolated transformed host cell according to claim 11, whereinsaid polynucleotide encodes said HLA binding fragment.
 14. The isolatedtransformed host cell according to claim 11, wherein said polynucleotideis complementary along the full length of said polynucleotide of a). 15.The isolated transformed host cell according to claim 11, wherein saidpolynucleotide is complementary along the full length of thepolynucleotide of b).
 16. The isolated transformed host cell accordingto claim 11, wherein said polynucleotide is a vector comprising apromoter operably linked to a polynucleotide: a) encoding a polypeptidecomprising SEQ ID NO: 2; b) encoding a Human Leukocyte Antigen (HLA)binding fragment of SEQ ID NO: 2, said fragment comprising at least fiveconsecutive amino acids of SEQ ID NO: 2; or c) that is complementaryalong the full length of said polynucleotide of a) or b).
 17. Theisolated transformed host cell according to claim 16, wherein saidpolynucleotide encodes said polypeptide comprising SEQ ID NO:
 2. 18. Theisolated transformed host cell according to claim 16, wherein saidpolynucleotide encodes said HLA binding fragment.
 19. The isolatedtransformed host cell according to claim 16, wherein said polynucleotideis complementary along the full length of said polynucleotide of a). 20.The isolated transformed host cell according to claim 16, wherein saidpolynucleotide is complementary along the full length of saidpolynucleotide of b).
 21. A method of making a polypeptide, comprisingculturing an isolated transformed host cell according to claim 11 underconditions that allow for the production of said polypeptide.
 22. Theisolated or purified polynucleotide according to claim 1, wherein saidHLA binding fragment has a length selected from the group consisting of8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 33, 34, and 35 amino acids.
 23. The vectoraccording to claim 6, wherein said HLA binding fragment has a lengthselected from the group consisting of 8, 9, 10, 11, 12, 13, 14, 15, 16,17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,and 35 amino acids.
 24. The isolated transformed host cell according toclaim 11, wherein said HLA binding fragment has a length selected fromthe group consisting of 8, 9,
 10. 11, 12, 13, 14, 15, 16, 17, 18, 19,20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, and 35 aminoacids.
 25. The isolated transformed host cell according to claim 16,wherein said HLA binding fragment has a length selected from the groupconsisting of 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, and 35 amino acids.